From 06eb8eacf0977961f5bc145a597538f097896590 Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Mon, 26 Jun 2023 09:59:37 -0700
Subject: [PATCH 01/41] initial commit on the branch

---
 .github/workflows/release.yml             |  2 +-
 main.nf                                   |  2 +-
 modules/convert.nf                        | 61 +++++++++++++++++++++++
 modules/msconvert.nf                      | 29 -----------
 subworkflows/{msconvert.nf => convert.nf} | 15 +++++-
 tests/conftest.py                         | 15 +++++-
 6 files changed, 90 insertions(+), 34 deletions(-)
 create mode 100644 modules/convert.nf
 delete mode 100644 modules/msconvert.nf
 rename subworkflows/{msconvert.nf => convert.nf} (68%)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 4a7121d..d24dc05 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Create latest tag
         uses: Actions-R-Us/actions-tagger@latest
diff --git a/main.nf b/main.nf
index 3b2be0a..4a87261 100644
--- a/main.nf
+++ b/main.nf
@@ -3,7 +3,7 @@
 nextflow.enable.dsl = 2
 
 // Subworkflows
-include { CONVERT_TO_MZML } from "./subworkflows/msconvert"
+include { CONVERT_TO_MZML } from "./subworkflows/convert"
 include {
     BUILD_CHROMATOGRAM_LIBRARY;
     PERFORM_QUANT;
diff --git a/modules/convert.nf b/modules/convert.nf
new file mode 100644
index 0000000..3e41acd
--- /dev/null
+++ b/modules/convert.nf
@@ -0,0 +1,61 @@
+process MSCONVERT {
+    publishDir "${params.mzml_dir}/${outputDir}", failOnError: true
+    label 'process_low_constant'
+    label 'error_retry'
+
+    input:
+        tuple val(file_id), path(raw_input), val(outputDir)
+
+    output:
+        tuple val(file_id), path("${raw_input.baseName}.mzML.gz")
+
+    script:
+    """
+    wine msconvert \\
+        -v \\
+        --gzip \\
+        --mzML \\
+        --64 \\
+        --zlib \\
+        --filter "peakPicking true 1-" \\
+        ${params.msconvert.demultiplex ? '--filter "demultiplex optimization=overlap_only"' : ''} \\
+        ${raw_input}
+    """
+
+    stub:
+    """
+    touch ${raw_input.baseName}.mzML.gz
+    """
+}
+
+
+process TDF2MZML {
+    publishDir "${params.mzml_dir}/${outputDir}", pattern: "*.mzML.gz", failOnError: true
+    container 'mfreitas/tdf2mzml:latest' // I don't know which stable tag to use...
+    label 'process_single'
+    label 'error_retry'
+
+    input:
+        tuple val(file_id), path(tdf_input), val(outputDir)
+
+    output:
+    tuple val(file_id), path("${file(tdf_input.baseName).baseName}.mzML.gz")
+
+    script:
+    """
+    echo "Unpacking..."
+    tar -xvf ${tdf_input}
+
+    echo "Converting..."
+    tdf2mzml.py -i *.d # --ms1_type "centroid"
+
+    echo "Compressing..."
+    mv *.mzml ${file(tdf_input.baseName).baseName}.mzML
+    gzip ${file(tdf_input.baseName).baseName}.mzML
+    """
+
+    stub:
+    """
+    touch ${file(tdf_input.baseName).baseName}.mzML.gz
+    """
+}
\ No newline at end of file
diff --git a/modules/msconvert.nf b/modules/msconvert.nf
deleted file mode 100644
index b3430c3..0000000
--- a/modules/msconvert.nf
+++ /dev/null
@@ -1,29 +0,0 @@
-process MSCONVERT {
-    publishDir "${params.mzml_dir}/${outputDir}", failOnError: true
-    label 'process_low_constant'
-    label 'error_retry'
-
-    input:
-        tuple val(file_id), path(raw_input), val(outputDir)
-
-    output:
-        tuple val(file_id), path("${raw_input.baseName}.mzML.gz")
-
-    script:
-    """
-    wine msconvert \\
-        -v \\
-        --gzip \\
-        --mzML \\
-        --64 \\
-        --zlib \\
-        --filter "peakPicking true 1-" \\
-        ${params.msconvert.demultiplex ? '--filter "demultiplex optimization=overlap_only"' : ''} \\
-        ${raw_input}
-    """
-
-    stub:
-    """
-    touch ${raw_input.baseName}.mzML.gz
-    """
-}
diff --git a/subworkflows/msconvert.nf b/subworkflows/convert.nf
similarity index 68%
rename from subworkflows/msconvert.nf
rename to subworkflows/convert.nf
index 1d889d7..8cd1e30 100644
--- a/subworkflows/msconvert.nf
+++ b/subworkflows/convert.nf
@@ -1,6 +1,7 @@
-include { MSCONVERT } from "../modules/msconvert.nf"
 
 
+include { MSCONVERT; TDF2MZML } from "../modules/convert"
+
 workflow CONVERT_TO_MZML {
     take:
     raw_files
@@ -21,7 +22,17 @@ workflow CONVERT_TO_MZML {
     }
     | set { staging }
 
-    MSCONVERT(staging.mzml_absent)
+    staging.mzml_absent
+    | branch {
+        is_tdf: it[0].toLowerCase().endsWith(".d.tar")
+        return it
+        is_raw: true
+        return it
+    }
+    |set { to_convert }
+
+    MSCONVERT(to_convert.is_raw)
+    | concat(TDF2MZML(to_convert.is_tdf))
     | concat(staging.is_mzml)
     | concat(staging.mzml_present)
     | set { results }
diff --git a/tests/conftest.py b/tests/conftest.py
index 06ff8c6..03cd4eb 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -14,18 +14,31 @@ def base_project(tmp_path):
     raw_dir = tmp_path / "subdir"
     raw_dir.mkdir()
     raw_files = [raw_dir / f"{f}.raw" for f in "abcdefghijklm"]
+    dot_d_files = [raw_dir / f"{f}.d.tar" for f in "opqrs"]
     for raw_file in raw_files:
         raw_file.touch()
+    for raw_file in dot_d_files:
+        raw_file.touch()
 
     mzml_file = raw_dir / "n.mzML.gz"
     mzml_file.touch()
     raw_files.append(mzml_file)
+    raw_files.extend(dot_d_files)
 
     chrlibs = ["true"] * 6 + ["false"] * 8
-    groups = "xyz" * 4 + "z" * 2
+    chrlibs.extend(["false"] * len(dot_d_files))
+    groups = "xyz" * 4 + "z" * 2 + "" * 8 + "w" * len(dot_d_files)
 
     # create an input csv
     ms_files = ["file,chrlib,group"]
+
+    # This assertion makes sure we are defining the
+    # csv correctly and does not get prematurely terminated
+    # since zip does not check that all arguments are the same
+    # length.
+    assert len(raw_files) == len(chrlibs)
+    assert len(raw_files) == len(groups)
+
     for row in zip(raw_files, chrlibs, groups):
         row = list(row)
         row[0] = str(row[0])

From c4c15918d6242217d9498ec768d3162e6c17098c Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Tue, 27 Jun 2023 11:19:42 -0700
Subject: [PATCH 02/41] added params to the encyclopedia run

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 0acaf12..c952eda 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -88,7 +88,7 @@ params {
      *  The default attempts to match the defaults from the graphical
      *  user interface.
      */
-    encyclopedia.args = '-percolatorVersion v3-01 -quantifyAcrossSamples true -scoringBreadthType window'
+    encyclopedia.args = '-percolatorVersion v3-01 -quantifyAcrossSamples true -scoringBreadthType window -minLength 7 -maxLength 40 -minIntensity 50 -filterPeaklists true '
 
     /** Additional command line arguments to use when searching files. */
     encyclopedia.local.args = ''

From 6a19f136521ac84096ae1dddae85b9fe7a55fd49 Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Fri, 21 Jul 2023 11:54:55 -0700
Subject: [PATCH 03/41] (wip) addition of skyline

---
 main.nf                          |  49 +++++++++++++-
 modules/encyclopedia.nf          |   6 +-
 modules/ims.nf                   |  23 +++++++
 modules/skyline.nf               | 113 +++++++++++++++++++++++++++++++
 subworkflows/encyclopedia.nf     |  16 ++++-
 tests/conftest.py                |   3 +
 tests/system_tests/test_stubs.py |  10 +++
 7 files changed, 216 insertions(+), 4 deletions(-)
 create mode 100644 modules/ims.nf
 create mode 100644 modules/skyline.nf

diff --git a/main.nf b/main.nf
index 4a87261..60b52b7 100644
--- a/main.nf
+++ b/main.nf
@@ -12,6 +12,12 @@ include {
 
 // Modules
 include { MSSTATS } from "./modules/msstats"
+include { ADD_IMS_INFO } from "./modules/ims"
+include { 
+    SKYLINE_ADD_LIB;
+    SKYLINE_IMPORT_DATA;
+    SKYLINE_MERGE_RESULTS
+} from "./modules/skyline"
 
 
 //
@@ -74,6 +80,16 @@ workflow {
         error "No MS data files were provided. Nothing to do."
     }
 
+    // Raw Mass Spec files (raw including .raw or .d/.tar)
+    // These files will be used later to quant using skyline.
+    // This also filter out files that are chromatogram libraries
+    ms_files.runs
+    | join(ms_files.meta)
+    | filter { !it[1] }
+    | map { it[0] }
+    | filter( ~/^.*((.raw)|(.d.tar))$/ )
+    | set { raw_quant_files }
+
     // Convert raw files to gzipped mzML and group them by experiment.
     // The chrlib and quant channels take the following form:
     // [[file_ids], [mzml_gz_files], is_chrlib, group]
@@ -111,9 +127,38 @@ workflow {
     if ( params.aggregate ) {
         // Aggregate quantitative runs with EncyclopeDIA.
         // The output has one channel:
-        // global -> [agg_name, peptides, proteins] or null
+        // global -> [agg_name, peptides_txt, proteins_txt] or null
+        // lib -> blib
         PERFORM_AGGREGATE_QUANT(quant_results.local, dlib, fasta)
         | set { enc_results }
+        
+        ADD_IMS_INFO(enc_results.blib)
+        | set { blib }
+
+        skyline_template = file(params.skyline_template, checkIfExists: true)
+        SKYLINE_ADD_LIB(skyline_template, blib, fasta)
+        | set { skyline_template_zipfile }
+
+        SKYLINE_IMPORT_DATA(
+            skyline_template_zipfile.skyline_zipfile,
+            raw_quant_files,
+        )
+        | set { skyline_import_results }
+
+        raw_quant_files = raw_quant_files.collect()
+
+        skyline_import_results.skyd_file.view()
+        skyd_files = skyline_import_results.skyd_file.collect()
+
+        skyd_files.view()
+
+        SKYLINE_MERGE_RESULTS(
+            skyline_template_zipfile.skyline_zipfile,
+            skyd_files,
+            raw_quant_files,
+        )
+
+
     } else {
         quant_results | set{ enc_results }
     }
@@ -122,6 +167,8 @@ workflow {
     if ( params.msstats.enabled ) {
         MSSTATS(enc_results.global, input, contrasts)
     }
+
+    // 
 }
 
 
diff --git a/modules/encyclopedia.nf b/modules/encyclopedia.nf
index 01bd427..e25e012 100644
--- a/modules/encyclopedia.nf
+++ b/modules/encyclopedia.nf
@@ -23,7 +23,7 @@ def stem(suffix) {
 process ENCYCLOPEDIA_SEARCH {
     publishDir "${params.result_dir}/${group}/elib", pattern: '*.elib', failOnError: true
     publishDir "${params.result_dir}/${group}/logs", pattern: '*.log', failOnError: true
-    label 'process_medium'
+    label 'process_high'
 
     input:
         tuple val(group), path(mzml_gz_file)
@@ -70,6 +70,7 @@ process ENCYCLOPEDIA_SEARCH {
 
 process ENCYCLOPEDIA_AGGREGATE {
     publishDir "${params.result_dir}/${group}/elib", pattern: '*.elib', failOnError: true
+    publishDir "${params.result_dir}/${group}/blib", pattern: '*.blib', failOnError: true
     publishDir "${params.result_dir}/${group}/logs", pattern: '*.log', failOnError: true
     publishDir "${params.result_dir}/${group}/results", pattern: '*.txt', failOnError: true
     publishDir "${params.result_dir}/${group}/reports", pattern: '*.csv', failOnError: true
@@ -92,6 +93,7 @@ process ENCYCLOPEDIA_AGGREGATE {
         tuple(
             val(group),
             path("${stem(output_suffix)}.elib"),
+            path("${stem(output_suffix)}.blib"),
             path("${stem(output_suffix)}.global.log"),
             path("${output_suffix}_detection_summary.csv"),
             emit: "lib"
@@ -117,6 +119,7 @@ process ENCYCLOPEDIA_AGGREGATE {
         -i ./ \\
         -f ${fasta_file} \\
         -l ${library_file} \\
+        -blib true \\
         ${params.encyclopedia.args} \\
         ${params.encyclopedia.global.args} \\
         -a ${align} \\
@@ -140,6 +143,7 @@ process ENCYCLOPEDIA_AGGREGATE {
     stub:
     """
     touch ${stem(output_suffix)}.elib
+    touch ${stem(output_suffix)}.blib
 
     if [ "${align}" = true ]; then
         touch ${stem(output_suffix)}.peptides.txt
diff --git a/modules/ims.nf b/modules/ims.nf
new file mode 100644
index 0000000..d315df2
--- /dev/null
+++ b/modules/ims.nf
@@ -0,0 +1,23 @@
+
+process ADD_IMS_INFO {
+    publishDir "${params.result_dir}/${group}/blib", pattern: '*.ims.blib', failOnError: true
+    label 'process_medium'
+    container 'ghcr.io/talusbio/flimsay:v0.2.0'
+
+    input:
+        path blib
+
+    output:
+        path("*.ims.blib"), emit: blib
+
+    script:
+    """
+    flimsay fill_blib ${blib} blib.ims.blib 
+    """
+
+    stub:
+    """
+    echo "${blib}"
+    touch blib.ims.blib
+    """
+}
diff --git a/modules/skyline.nf b/modules/skyline.nf
new file mode 100644
index 0000000..5eba01a
--- /dev/null
+++ b/modules/skyline.nf
@@ -0,0 +1,113 @@
+process SKYLINE_ADD_LIB {
+    publishDir "${params.result_dir}/skyline/add-lib", failOnError: true, mode: 'copy'
+    label 'process_medium'
+    label 'error_retry'
+    container 'quay.io/protio/pwiz-skyline-i-agree-to-the-vendor-licenses:3.0.23187-2243781'
+
+    input:
+        path skyline_template_zipfile
+        path fasta
+        path blib
+
+    output:
+        path("results.sky.zip"), emit: skyline_zipfile
+        path("skyline_add_library.log"), emit: log
+
+    script:
+    """
+    unzip ${skyline_template_zipfile}
+
+    wine SkylineCmd \
+        --in="${skyline_template_zipfile.baseName}" \
+        --log-file=skyline_add_library.log \
+        --import-fasta="${fasta}" \
+        --add-library-path="${blib}" \
+        --out="results.sky" \
+        --save \
+        --share-zip="results.sky.zip" \
+        --share-type="complete"
+    """
+
+    stub:
+    """
+    echo "${skyline_template_zipfile}"
+    echo "${fasta}"
+    echo "${blib}"
+    touch skyline_add_library.log
+    touch results.sky.zip
+    """
+}
+
+process SKYLINE_IMPORT_DATA {
+    publishDir "${params.result_dir}/skyline/import-spectra", failOnError: true, mode: 'copy'
+    label 'process_medium'
+    label 'process_high_memory'
+    label 'error_retry'
+    container 'quay.io/protio/pwiz-skyline-i-agree-to-the-vendor-licenses:3.0.23187-2243781'
+
+    input:
+        path skyline_zipfile
+        path raw_file
+
+    output:
+        path("*.skyd"), emit: skyd_file
+        path("${raw_file.baseName}.log"), emit: log_file
+
+    script:
+    """
+    unzip ${skyline_zipfile}
+
+    wine SkylineCmd \
+        --in="${skyline_zipfile.baseName}" \
+        --import-no-join \
+        --log-file="${raw_file.baseName}.log" \
+        --import-file="${raw_file}" \
+    """
+
+    stub:
+    """
+    echo "${skyline_zipfile}"
+    echo "${raw_file}"
+    touch ${raw_file.baseName}.skyd
+    touch ${raw_file.baseName}.log
+    """
+}
+
+process SKYLINE_MERGE_RESULTS {
+    publishDir "${params.result_dir}/skyline/import-spectra", failOnError: true, mode: 'copy'
+    label 'process_high'
+    label 'error_retry'
+    container 'quay.io/protio/pwiz-skyline-i-agree-to-the-vendor-licenses:3.0.23187-2243781'
+
+    input:
+        path skyline_zipfile
+        path '*.skyd'
+        val raw_files
+
+    output:
+        path("final.sky.zip"), emit: final_skyline_zipfile
+        path("skyline-merge.log"), emit: log
+
+    script:
+    // import_files_params = "--import-file=${(mzml_files as List).collect{ "/tmp/" + file(it).name }.join(' --import-file=')}"
+    """
+    unzip ${skyline_zipfile}
+
+    wine SkylineCmd \
+        --in="${skyline_zipfile.baseName}" \
+        --log-file="skyline-merge.log" \
+        ${import_files_params} \
+        --out="final.sky" \
+        --save \
+        --share-zip="final.sky.zip" \
+        --share-type="complete"
+    """
+
+    stub:
+    """
+    echo "${skyline_zipfile}"
+    echo "${*.skyd}"
+    touch skyline-merge.log
+    touch final.sky.zip
+    """
+}
diff --git a/subworkflows/encyclopedia.nf b/subworkflows/encyclopedia.nf
index fda0e44..8ac919f 100644
--- a/subworkflows/encyclopedia.nf
+++ b/subworkflows/encyclopedia.nf
@@ -97,7 +97,10 @@ workflow PERFORM_QUANT {
                 fasta,
                 params.encyclopedia.quant_suffix,
                 true  // Align RTs
-            ).quant
+            )
+            | set { agg_outs }
+            
+            agg_outs.quant
             | set { global_files }
         }
 
@@ -136,9 +139,18 @@ workflow PERFORM_AGGREGATE_QUANT {
             fasta,
             params.encyclopedia.quant_suffix,
             true  // Align RTs
-        ).quant
+        ) 
+        | set { agg_results }
+        
+        agg_results.quant
         | set { global_files }
 
+        // Lib is ['aggregated', .elib, .blib, .log, summary.csv]
+        agg_results.lib
+        | map {it[1]}
+        | set { blib }
+
     emit:
         global = global_files
+        blib = blib
 }
diff --git a/tests/conftest.py b/tests/conftest.py
index 03cd4eb..8718087 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -47,6 +47,9 @@ def base_project(tmp_path):
     ms_files_csv = tmp_path / "ms_files.csv"
     with ms_files_csv.open("w+") as fhndl:
         fhndl.write("\n".join(ms_files) + "\n")
+    
+    # print the file
+    print(ms_files_csv.read_text())
 
     ms_files_csv_short = tmp_path / "ms_files_short.csv"
     with ms_files_csv_short.open("w+") as fhndl:
diff --git a/tests/system_tests/test_stubs.py b/tests/system_tests/test_stubs.py
index ff318ab..f08e9f1 100644
--- a/tests/system_tests/test_stubs.py
+++ b/tests/system_tests/test_stubs.py
@@ -9,6 +9,7 @@ def test_no_groups(base_project, tmp_path):
     config, input_csv, _ = base_project
     pd.read_csv(input_csv).drop(columns="group").to_csv(input_csv, index=False)
     cmd = ["nextflow", "run", "main.nf"] + config
+    print(cmd)
     subprocess.run(cmd, check=True)
     base = tmp_path / "results"
 
@@ -19,6 +20,7 @@ def test_no_aggregate(base_project, tmp_path):
     """Test the workflow logic for per experiment workflows"""
     config, *_ = base_project
     cmd = ["nextflow", "run", "main.nf"] + config
+    print(cmd)
     subprocess.run(cmd, check=True)
     base = tmp_path / "results"
     expected = [
@@ -45,16 +47,22 @@ def test_aggregate(base_project, tmp_path):
     """Test workflow logic for global analyses."""
     config, *_ = base_project
 
+    template_file = tmp_path / "template.sky.zip"
+    template_file.touch()
+
     cmd = [
         "nextflow",
         "run",
         "main.nf",
         "--aggregate",
         "true",
+        "--skyline_template",
+        str(template_file),
     ]
 
     cmd += config
 
+    print(cmd)
     subprocess.run(cmd, check=True)
     base = tmp_path / "results"
     not_expected = [
@@ -80,6 +88,7 @@ def test_already_converted(base_project, tmp_path):
 
     config, *_ = base_project
     cmd = ["nextflow", "run", "main.nf"] + config
+    print(cmd)
     subprocess.run(cmd, check=True)
 
     assert old == mzml.stat()
@@ -96,6 +105,7 @@ def test_force_convert(base_project, tmp_path):
 
     config, *_ = base_project
     cmd = ["nextflow", "run", "main.nf", "--msconvert.force", "true"] + config
+    print(cmd)
     subprocess.run(cmd, check=True)
 
     assert old != mzml.stat()

From 96a8b3e06b2b35b64fcb725adbb13be025a1cf84 Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Fri, 21 Jul 2023 13:51:44 -0700
Subject: [PATCH 04/41] added branching to the skyline quant step

---
 main.nf            | 12 ++++++++----
 modules/ims.nf     |  3 ++-
 modules/skyline.nf |  6 ++----
 3 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/main.nf b/main.nf
index 60b52b7..6607e0e 100644
--- a/main.nf
+++ b/main.nf
@@ -131,14 +131,20 @@ workflow {
         // lib -> blib
         PERFORM_AGGREGATE_QUANT(quant_results.local, dlib, fasta)
         | set { enc_results }
-        
-        ADD_IMS_INFO(enc_results.blib)
+
+        quant_results.local
+        | map { it[0] }
+        | set { groups }
+
+        ADD_IMS_INFO(groups, enc_results.blib)
         | set { blib }
 
         skyline_template = file(params.skyline_template, checkIfExists: true)
         SKYLINE_ADD_LIB(skyline_template, blib, fasta)
         | set { skyline_template_zipfile }
 
+        println raw_quant_files
+        raw_quant_files.view()
         SKYLINE_IMPORT_DATA(
             skyline_template_zipfile.skyline_zipfile,
             raw_quant_files,
@@ -147,9 +153,7 @@ workflow {
 
         raw_quant_files = raw_quant_files.collect()
 
-        skyline_import_results.skyd_file.view()
         skyd_files = skyline_import_results.skyd_file.collect()
-
         skyd_files.view()
 
         SKYLINE_MERGE_RESULTS(
diff --git a/modules/ims.nf b/modules/ims.nf
index d315df2..a537c9a 100644
--- a/modules/ims.nf
+++ b/modules/ims.nf
@@ -5,6 +5,7 @@ process ADD_IMS_INFO {
     container 'ghcr.io/talusbio/flimsay:v0.2.0'
 
     input:
+        val group
         path blib
 
     output:
@@ -12,7 +13,7 @@ process ADD_IMS_INFO {
 
     script:
     """
-    flimsay fill_blib ${blib} blib.ims.blib 
+    flimsay fill_blib ${blib} blib.ims.blib
     """
 
     stub:
diff --git a/modules/skyline.nf b/modules/skyline.nf
index 5eba01a..ff51441 100644
--- a/modules/skyline.nf
+++ b/modules/skyline.nf
@@ -47,7 +47,7 @@ process SKYLINE_IMPORT_DATA {
 
     input:
         path skyline_zipfile
-        path raw_file
+        each path(raw_file)
 
     output:
         path("*.skyd"), emit: skyd_file
@@ -89,7 +89,7 @@ process SKYLINE_MERGE_RESULTS {
         path("skyline-merge.log"), emit: log
 
     script:
-    // import_files_params = "--import-file=${(mzml_files as List).collect{ "/tmp/" + file(it).name }.join(' --import-file=')}"
+    import_files_params = "--import-file=${(mzml_files as List).collect{ "/tmp/" + file(it).name }.join(' --import-file=')}"
     """
     unzip ${skyline_zipfile}
 
@@ -105,8 +105,6 @@ process SKYLINE_MERGE_RESULTS {
 
     stub:
     """
-    echo "${skyline_zipfile}"
-    echo "${*.skyd}"
     touch skyline-merge.log
     touch final.sky.zip
     """

From 0a76604f863dec6502345ce375326ed0e178d46c Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Fri, 21 Jul 2023 14:34:49 -0700
Subject: [PATCH 05/41] (wip) improvement on skyline job passing

---
 main.nf            | 7 +++----
 modules/skyline.nf | 6 +++---
 2 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/main.nf b/main.nf
index 6607e0e..b901c9d 100644
--- a/main.nf
+++ b/main.nf
@@ -143,8 +143,7 @@ workflow {
         SKYLINE_ADD_LIB(skyline_template, blib, fasta)
         | set { skyline_template_zipfile }
 
-        println raw_quant_files
-        raw_quant_files.view()
+        // This will generate a skyd for every raw data file
         SKYLINE_IMPORT_DATA(
             skyline_template_zipfile.skyline_zipfile,
             raw_quant_files,
@@ -152,16 +151,16 @@ workflow {
         | set { skyline_import_results }
 
         raw_quant_files = raw_quant_files.collect()
-
         skyd_files = skyline_import_results.skyd_file.collect()
-        skyd_files.view()
 
         SKYLINE_MERGE_RESULTS(
             skyline_template_zipfile.skyline_zipfile,
             skyd_files,
             raw_quant_files,
         )
+        | set { skyline_merge_results }
 
+        skyline_merge_results.final_skyline_zipfile.view()
 
     } else {
         quant_results | set{ enc_results }
diff --git a/modules/skyline.nf b/modules/skyline.nf
index ff51441..9747e2b 100644
--- a/modules/skyline.nf
+++ b/modules/skyline.nf
@@ -1,5 +1,5 @@
 process SKYLINE_ADD_LIB {
-    publishDir "${params.result_dir}/skyline/add-lib", failOnError: true, mode: 'copy'
+    publishDir "${params.result_dir}/skyline/", failOnError: true, mode: 'copy'
     label 'process_medium'
     label 'error_retry'
     container 'quay.io/protio/pwiz-skyline-i-agree-to-the-vendor-licenses:3.0.23187-2243781'
@@ -39,7 +39,7 @@ process SKYLINE_ADD_LIB {
 }
 
 process SKYLINE_IMPORT_DATA {
-    publishDir "${params.result_dir}/skyline/import-spectra", failOnError: true, mode: 'copy'
+    publishDir "${params.result_dir}/skyline/", failOnError: true, mode: 'copy'
     label 'process_medium'
     label 'process_high_memory'
     label 'error_retry'
@@ -74,7 +74,7 @@ process SKYLINE_IMPORT_DATA {
 }
 
 process SKYLINE_MERGE_RESULTS {
-    publishDir "${params.result_dir}/skyline/import-spectra", failOnError: true, mode: 'copy'
+    publishDir "${params.result_dir}/skyline/", failOnError: true, mode: 'copy'
     label 'process_high'
     label 'error_retry'
     container 'quay.io/protio/pwiz-skyline-i-agree-to-the-vendor-licenses:3.0.23187-2243781'

From 84dc60a333099cd0149a2b2e4ba28f730119428c Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Mon, 24 Jul 2023 11:34:06 -0700
Subject: [PATCH 06/41] made blib conversion 2 step

---
 modules/encyclopedia.nf | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/modules/encyclopedia.nf b/modules/encyclopedia.nf
index e25e012..b2e3dc8 100644
--- a/modules/encyclopedia.nf
+++ b/modules/encyclopedia.nf
@@ -119,12 +119,14 @@ process ENCYCLOPEDIA_AGGREGATE {
         -i ./ \\
         -f ${fasta_file} \\
         -l ${library_file} \\
-        -blib true \\
         ${params.encyclopedia.args} \\
         ${params.encyclopedia.global.args} \\
         -a ${align} \\
     | tee ${stem(output_suffix)}.global.log
 
+    ${execEncyclopedia(task.memory)} \\
+        -convert -libtoblib -i ${stem(output_suffix)}.elib
+
     # Better file names:
     if [ "${align}" = true ]; then
         mv ${stem(output_suffix)}.elib.peptides.txt ${stem(output_suffix)}.peptides.txt

From fa5bf4b7ae6f997f62a24c313abe37d1a01aca65 Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@users.noreply.github.com>
Date: Mon, 24 Jul 2023 11:47:39 -0700
Subject: [PATCH 07/41] Update test.yml

---
 .github/workflows/test.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 307ea52..bd9b511 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -39,9 +39,9 @@ jobs:
 
     - name: Run Unit Tests
       run: |
-        REMOTE=/app/nf-encyclopedia
-        docker run -v $(pwd):${REMOTE} -w ${REMOTE} nf-encyclopedia:latest \
-          pytest tests/unit_tests
+        # REMOTE=/app/nf-encyclopedia
+        docker run -v $(pwd):${REMOTE} nf-encyclopedia:latest \
+          pytest tests/unit_tests # -w ${REMOTE}
 
     - name: Run System Tests
       run: |

From d9706cee5f70cbb2e6bb6392d8ad1045c8c88ab3 Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Mon, 24 Jul 2023 11:54:35 -0700
Subject: [PATCH 08/41] minor addition to tests cicd

---
 .github/workflows/test.yml   |  2 +-
 subworkflows/encyclopedia.nf | 26 +++++++++++++-------------
 2 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index bd9b511..3bd8cde 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -39,7 +39,7 @@ jobs:
 
     - name: Run Unit Tests
       run: |
-        # REMOTE=/app/nf-encyclopedia
+        REMOTE=/app/nf-encyclopedia
         docker run -v $(pwd):${REMOTE} nf-encyclopedia:latest \
           pytest tests/unit_tests # -w ${REMOTE}
 
diff --git a/subworkflows/encyclopedia.nf b/subworkflows/encyclopedia.nf
index 8ac919f..d3db851 100644
--- a/subworkflows/encyclopedia.nf
+++ b/subworkflows/encyclopedia.nf
@@ -41,7 +41,7 @@ workflow BUILD_CHROMATOGRAM_LIBRARY {
             params.encyclopedia.chrlib_suffix,
             false  // Don't align RTs
         ).lib
-        | map { it -> tuple it[0], it[1] }
+        | map { eait -> tuple eait[0], eait[1] }
         | set { output_elib }
 
     emit:
@@ -61,9 +61,9 @@ workflow PERFORM_QUANT {
         // output is [group, mzml_gz_file, elib]
         quant_files
         | transpose()
-        | multiMap { it ->
-            mzml: tuple it[0], it[1]
-            elib: it[2]
+        | multiMap { qit ->
+        mzml: tuple qit[0], qit[1]
+        elib: qit[2]
         }
         | set { ungrouped_files }
 
@@ -86,12 +86,12 @@ workflow PERFORM_QUANT {
 
         // Only run group-wise global if needed.
         if ( local_only ) {
-            Channel.empty() | set { global_files }
-            Channel.empty() | set { msstats_files }
+        Channel.empty() | set { global_files }
+        Channel.empty() | set { msstats_files }
         } else {
-            // Do the global analysis
-            // Output is [group, peptides_txt, proteins_txt]
-            ENCYCLOPEDIA_AGGREGATE(
+        // Do the global analysis
+        // Output is [group, peptides_txt, proteins_txt]
+        ENCYCLOPEDIA_AGGREGATE(
                 local_files,
                 dlib,
                 fasta,
@@ -100,7 +100,7 @@ workflow PERFORM_QUANT {
             )
             | set { agg_outs }
             
-            agg_outs.quant
+        agg_outs.quant
             | set { global_files }
         }
 
@@ -139,15 +139,15 @@ workflow PERFORM_AGGREGATE_QUANT {
             fasta,
             params.encyclopedia.quant_suffix,
             true  // Align RTs
-        ) 
+        )
         | set { agg_results }
-        
+
         agg_results.quant
         | set { global_files }
 
         // Lib is ['aggregated', .elib, .blib, .log, summary.csv]
         agg_results.lib
-        | map {it[1]}
+        | map { libe -> libe[1] }
         | set { blib }
 
     emit:

From df8e1ebc82988317d11745cc09af775617ea6483 Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Mon, 24 Jul 2023 15:47:00 -0700
Subject: [PATCH 09/41] updated docker image

---
 Dockerfile      | 69 ++++++++++++++++++++++++++++---------------------
 environment.yml | 12 ++++-----
 2 files changed, 46 insertions(+), 35 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 61ff417..ad7d099 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,66 +1,77 @@
 FROM --platform=linux/amd64 mambaorg/micromamba:latest as micromamba
-# First Stage of the build, gets the jar for encyclopedia
-FROM --platform=linux/amd64 openjdk:8-jre
+# FROM --platform=linux/amd64 ibmjava:11
+# FROM --platform=linux/amd64 amazoncorretto:11-al2023-headless # Uses yum for package management.
+FROM --platform=linux/amd64 nextflow/nextflow:23.04.2
+
 ARG VERSION=2.12.30
 ENV VERSION ${VERSION}
+LABEL authors="wfondrie@talus.bio" \
+      description="Docker image for most of nf-encyclopedia"
+
+
+# Install procps so that Nextflow can poll CPU usage and
+# deep clean the apt cache to reduce image/layer size
+# RUN apt-get install -y procps sqlite3 libgomp1 \
+#     && apt-get clean -y && rm -rf /var/lib/apt/lists/*
+RUN yum install -y wget
 
-RUN apt-get update && \
-    apt-get -y upgrade && \ 
-    apt-get -y install libgomp1 && \
-    apt-get clean
 
 WORKDIR /code
+# First Stage of the build, gets the jar for encyclopedia
 RUN wget https://bitbucket.org/searleb/encyclopedia/downloads/encyclopedia-${VERSION}-executable.jar
-WORKDIR /app
 
-LABEL authors="wfondrie@talus.bio" \
-      description="Docker image for most of nf-encyclopedia"
+# # Install nextflow
+# RUN wget -qO- https://get.nextflow.io | bash
+# RUN chmod +x nextflow
+# RUN mv nextflow /usr/local/bin/.
 
-# Install procps so that Nextflow can poll CPU usage and
-# deep clean the apt cache to reduce image/layer size
-RUN apt-get update \
-    && apt-get install -y procps sqlite3 \
-    && apt-get clean -y && rm -rf /var/lib/apt/lists/*
+WORKDIR /app
 
 # Setup micromamba:
-ARG MAMBA_USER=mamba
+ARG MAMBA_USER=root
 ARG MAMBA_USER_ID=1000
 ARG MAMBA_USER_GID=1000
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
 ENV MAMBA_USER=$MAMBA_USER
 ENV MAMBA_ROOT_PREFIX="/opt/conda"
 ENV MAMBA_EXE="/bin/micromamba"
+RUN mkdir -p ${MAMBA_ROOT_PREFIX} 
 
 COPY --from=micromamba "$MAMBA_EXE" "$MAMBA_EXE"
 COPY --from=micromamba /usr/local/bin/_activate_current_env.sh /usr/local/bin/_activate_current_env.sh
 COPY --from=micromamba /usr/local/bin/_dockerfile_shell.sh /usr/local/bin/_dockerfile_shell.sh
-COPY --from=micromamba /usr/local/bin/_entrypoint.sh /usr/local/bin/_entrypoint.sh
+COPY --from=micromamba /usr/local/bin/_entrypoint.sh /usr/local/bin/mamba_entrypoint.sh
 COPY --from=micromamba /usr/local/bin/_activate_current_env.sh /usr/local/bin/_activate_current_env.sh
 COPY --from=micromamba /usr/local/bin/_dockerfile_initialize_user_accounts.sh /usr/local/bin/_dockerfile_initialize_user_accounts.sh
 COPY --from=micromamba /usr/local/bin/_dockerfile_setup_root_prefix.sh /usr/local/bin/_dockerfile_setup_root_prefix.sh
 
-RUN /usr/local/bin/_dockerfile_initialize_user_accounts.sh && \
-    /usr/local/bin/_dockerfile_setup_root_prefix.sh
+# No need to set up accounts if we will run as root ...
+# RUN /usr/local/bin/_dockerfile_initialize_user_accounts.sh &&
+
+RUN /usr/local/bin/_dockerfile_setup_root_prefix.sh
 
 # Setup the environment
-USER root
+USER $MAMBA_USER
 COPY environment.yml /tmp/environment.yml
 
 # Instruct R processes to use these empty files instead of
 # clashing with a local one
 RUN touch .Rprofile .Renviron
 
-# Create the environment
-RUN micromamba install -y -n base -f /tmp/environment.yml && \
-    micromamba clean --all --yes
+# Set the path. NextFlow seems to circumvent the conda environment
+# We also need to set options for the JRE here.
+ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH:/bin" _JAVA_OPTIONS="-Djava.awt.headless=true" VERSION=$VERSION
 
 # Setup the EncyclopeDIA executable:
 RUN ln -s /code/encyclopedia-$VERSION-executable.jar /code/encyclopedia.jar
 
-# Set the path. NextFlow seems to circumvent the conda environment
-# We also need to set options for the JRE here.
-ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH" _JAVA_OPTIONS="-Djava.awt.headless=true" VERSION=$VERSION
-
 # Create the entrypoint:
-SHELL ["/usr/local/bin/_dockerfile_shell.sh"]
-ENTRYPOINT ["/usr/local/bin/_entrypoint.sh"]
-CMD []
+# SHELL ["/usr/local/bin/_dockerfile_shell.sh"]
+# ENTRYPOINT ["/usr/local/bin/mamba_entrypoint.sh", "/usr/local/bin/entry.sh"]
+
+# Create the environment
+RUN micromamba install -y -n base -f /tmp/environment.yml && \
+    micromamba clean --all --yes
+
+CMD ["/bin/bash"]
+
diff --git a/environment.yml b/environment.yml
index e8c1b41..c787b45 100644
--- a/environment.yml
+++ b/environment.yml
@@ -8,9 +8,9 @@ dependencies:
   - pytest
   - numpy
   - pandas
-  - bioconductor-msstats=4.2.0
-  - r-rlang
-  - r-dplyr
-  - r-tidyr
-  - r-magrittr
-  - r-stringr
+  - bioconda::bioconductor-msstats
+  - conda-forge::r-rlang
+  - conda-forge::r-dplyr
+  - conda-forge::r-tidyr
+  - r::r-magrittr
+  - r::r-stringr

From 2df5d7a0cc2b82ea114e10a4f96654321fd6003b Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Mon, 24 Jul 2023 15:49:59 -0700
Subject: [PATCH 10/41] moved skyline logic out of agg

---
 main.nf | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/main.nf b/main.nf
index b901c9d..8de8096 100644
--- a/main.nf
+++ b/main.nf
@@ -123,15 +123,6 @@ workflow {
     PERFORM_QUANT(quant_files, dlib, fasta, params.aggregate)
     | set { quant_results }
 
-    // Perform an aggregate analysis on all files if needed:
-    if ( params.aggregate ) {
-        // Aggregate quantitative runs with EncyclopeDIA.
-        // The output has one channel:
-        // global -> [agg_name, peptides_txt, proteins_txt] or null
-        // lib -> blib
-        PERFORM_AGGREGATE_QUANT(quant_results.local, dlib, fasta)
-        | set { enc_results }
-
         quant_results.local
         | map { it[0] }
         | set { groups }
@@ -162,6 +153,15 @@ workflow {
 
         skyline_merge_results.final_skyline_zipfile.view()
 
+    // Perform an aggregate analysis on all files if needed:
+    if ( params.aggregate ) {
+        // Aggregate quantitative runs with EncyclopeDIA.
+        // The output has one channel:
+        // global -> [agg_name, peptides_txt, proteins_txt] or null
+        // lib -> blib
+        PERFORM_AGGREGATE_QUANT(quant_results.local, dlib, fasta)
+        | set { enc_results }
+
     } else {
         quant_results | set{ enc_results }
     }

From f0559fa08157a8981a7798756e667ba2d9d04dd5 Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Mon, 24 Jul 2023 16:18:55 -0700
Subject: [PATCH 11/41] added skyline template asset

---
 .gitignore                   |  1 +
 main.nf                      | 47 ++++++++++++++++++------------------
 subworkflows/encyclopedia.nf |  6 ++++-
 3 files changed, 30 insertions(+), 24 deletions(-)

diff --git a/.gitignore b/.gitignore
index fc0d425..e8f2d3f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,5 @@
 .nextflow
+venv
 .Rhistory
 .idea/**
 .gradle
diff --git a/main.nf b/main.nf
index 8de8096..93947e6 100644
--- a/main.nf
+++ b/main.nf
@@ -55,6 +55,7 @@ workflow {
     input = file(params.input, checkIfExists: true)
     fasta = file(params.fasta, checkIfExists: true)
     dlib = file(params.dlib, checkIfExists: true)
+    skyline_empty_template = file("$baseDir/assets/template.sky.zip", checkIfExists: true)
 
     // Optional contrasts arg:
     if ( params.contrasts != null ) {
@@ -123,35 +124,35 @@ workflow {
     PERFORM_QUANT(quant_files, dlib, fasta, params.aggregate)
     | set { quant_results }
 
-        quant_results.local
-        | map { it[0] }
-        | set { groups }
+    quant_results.local
+    | map { it[0] }
+    | set { groups }
 
-        ADD_IMS_INFO(groups, enc_results.blib)
-        | set { blib }
+    // Add IMS info to the blib
+    ADD_IMS_INFO(groups, quant_results.blib)
+    | set { blib }
 
-        skyline_template = file(params.skyline_template, checkIfExists: true)
-        SKYLINE_ADD_LIB(skyline_template, blib, fasta)
-        | set { skyline_template_zipfile }
+    SKYLINE_ADD_LIB(skyline_empty_template, blib, fasta)
+    | set { skyline_template_zipfile }
 
-        // This will generate a skyd for every raw data file
-        SKYLINE_IMPORT_DATA(
-            skyline_template_zipfile.skyline_zipfile,
-            raw_quant_files,
-        )
-        | set { skyline_import_results }
+    // This will generate a skyd for every raw data file
+    SKYLINE_IMPORT_DATA(
+        skyline_template_zipfile.skyline_zipfile,
+        raw_quant_files,
+    )
+    | set { skyline_import_results }
 
-        raw_quant_files = raw_quant_files.collect()
-        skyd_files = skyline_import_results.skyd_file.collect()
+    raw_quant_files = raw_quant_files.collect()
+    skyd_files = skyline_import_results.skyd_file.collect()
 
-        SKYLINE_MERGE_RESULTS(
-            skyline_template_zipfile.skyline_zipfile,
-            skyd_files,
-            raw_quant_files,
-        )
-        | set { skyline_merge_results }
+    SKYLINE_MERGE_RESULTS(
+        skyline_template_zipfile.skyline_zipfile,
+        skyd_files,
+        raw_quant_files,
+    )
+    | set { skyline_merge_results }
 
-        skyline_merge_results.final_skyline_zipfile.view()
+    skyline_merge_results.final_skyline_zipfile.view()
 
     // Perform an aggregate analysis on all files if needed:
     if ( params.aggregate ) {
diff --git a/subworkflows/encyclopedia.nf b/subworkflows/encyclopedia.nf
index d3db851..103ef16 100644
--- a/subworkflows/encyclopedia.nf
+++ b/subworkflows/encyclopedia.nf
@@ -99,7 +99,10 @@ workflow PERFORM_QUANT {
                 true  // Align RTs
             )
             | set { agg_outs }
-            
+
+        agg_outs.lib |
+            map { libe -> libe[1] } |
+            set { global_blib }
         agg_outs.quant
             | set { global_files }
         }
@@ -107,6 +110,7 @@ workflow PERFORM_QUANT {
     emit:
         local = local_files
         global = global_files
+        blib = global_blib
 }
 
 

From f5b0d7fb8a0b3815f069dd2fdd42c47fd825543e Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Mon, 24 Jul 2023 16:21:41 -0700
Subject: [PATCH 12/41] handled no-merge use case

---
 subworkflows/encyclopedia.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/subworkflows/encyclopedia.nf b/subworkflows/encyclopedia.nf
index 103ef16..9f7f15f 100644
--- a/subworkflows/encyclopedia.nf
+++ b/subworkflows/encyclopedia.nf
@@ -88,6 +88,7 @@ workflow PERFORM_QUANT {
         if ( local_only ) {
         Channel.empty() | set { global_files }
         Channel.empty() | set { msstats_files }
+        Channel.empty() | set { global_blib }
         } else {
         // Do the global analysis
         // Output is [group, peptides_txt, proteins_txt]

From a1768bae0e9c0c0d2a1a3b1bccf72b8cf4419d77 Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Mon, 24 Jul 2023 16:26:46 -0700
Subject: [PATCH 13/41] added asset

---
 assets/template.sky.zip | Bin 0 -> 9127 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 assets/template.sky.zip

diff --git a/assets/template.sky.zip b/assets/template.sky.zip
new file mode 100644
index 0000000000000000000000000000000000000000..60e729ace70f78d8c4486d88dd253b5f20a59696
GIT binary patch
literal 9127
zcma)?Wo%v9(x&a0nVC6`8DnOMnVB($V~UxXnVH#+WA^beGc!ZX%*-_D{-&kAcQl&W
zTdI23($c%6{o~PARVm6qKw^S{fx&`(vT;@$k1+L-g8~El%?k#G2F3;EWM*RzFmf_u
zbhLJ7bg?vZO;1PtbND|WcrenxH^9Mg!SFaYr>@?X!2iiXd4`F9t<Q99>{dBZJ0>CS
zN#?w5(NFqa5KS4fiiY7Eq~hEN7MOxHT5XsY?=eeHpg-<iP+}A4hbb9W>qN`~Nma;W
z2X`D@y|_m<I*6wopG9&l#E`v9$by|Df$aG#Z{GytWM1Zkj`K`qFX9A+j?x6|kNC$A
z`Oo|-f`JFOQ5~fhhhaIScCqrpPv8$x&zn9-$1KfUL%DvlBxod|K6|C$KR!fOk%6qx
z21+l)*SFom(!2KOu)6o4V1TE><Bu{KL6um>BaR%8+XVTzj-ES$k%=QHz0HpOI-IzE
z;U}tV58WAv?_^t4K1`RZqR;q8w2xUVFw4>{cg=ztajLh9r0yYYsAcfWzASn8i{4Nf
z4|(m|9`%?u5DlL;kU1P+-0YMHxCPb;n%59>ttHM1QxZe*EuV>JEQME0ir929Zbx+s
z5j>QrPo)+*B#DfK>mjL>O54S<8L?ocqKI@Qr)Gn=zX`bh1i|UdM;*26BB?RJc<{+J
z^I9-1j1x)Q*@x1;<n)l+9g*CgLce_wWVD+d-DCVBn?XB<k05)4vn<L*^aq4(7#YJk
z>LPhWcoH|RnSG>BDQxm=c4RVphpSWW`K_YveLvN5b&I8)xD*KIqdpf;InHAiu^ooZ
zu4hs(%3cN%G$C)%k#UU~^|q^8rc8zvr?WMw*q#wRxM-pmh*&@H_RM;c^0h{(`%;yV
zP^44Gi7Wb4fR}Xar7cX$2SzaScN1L$W+pY)2;Xw9vo5jGIhc{#qt$VnC>9$Kxlzh-
zj%IClwNuCrDDDcU`)zkuQpj*fkqR0E*M^7$xPCA`lbE<BL^++|8!px&^Kvh6So>w`
zJg=L0-tM|-gr@gY0SuH0`MLMq8-=PX^ujDVH1k}uqC7(XTE0m*-0n7OgwEGm_fL>V
z<`6y{vsf?Hv<?-}47T(9OwdDc!8Kmc++39N0wSOAF9vuIu=>n+p0M06*RBq2)4TzR
zD?9332}|j<a(!srpD977OxYS)jtGI2F$QM40?~)U`}DhpN9>e(__+o2x$(^-Yzb)s
zzC7r;ufLg<3mBAA1nWm~w@j&Y1cs+Ab*QQ;^y3|~ty35>Q-MwM-v%&Q1S%aIk(&27
z+VFw=NT24(4%9=kzQg^{ml|@{-i^p=F>`-Pw(Mrwe28S*|G2B6<A+>0%=e*?a-?#J
zT=q^KdMYMcWSkD!Nj`l3%|``PH}kO3Dp<^;Y<H2KukeYk4_Ciix7y#QYd$)w0w7ol
zvLZMju}x5Oq9<8VjHBE1ag5EH=?rgC)F;T@<<+6RS#)#+19+^<PetuOW;&9ChD0Y9
zqNcyMjTZHu-OW`_XF$tCqEV{^`#h?bqbff!9EYCw2wIBbOumr0MLiuwg11t%7=}Ym
z`jbf*U(4tfiS5N}P<FgOXFZiTGd-~y_f<YP%upz0=uI0qG+0$cF;rc<>zRt|oqgfX
zgr=R{08eEq^`X?#n9wUIH#jIO0-R||Z^c@z>fi6TePBH(r~qWJFy>xLJ-(~X3CdBJ
zuzUb4ILz)Rf6#a0+oW$>9>WIc8ysuODtV`qbNAow36^y%;3+{=6?F*9KQSS$GE{s6
z*iU1$bCe$}7AzF4AJ{I|lTSCbF&w=t{%rHDm^p2s@BA_TabTskJ2FOg(LRU<1b34W
z^BUVyP(r_S2f7{GCkgL27U1c}mY+kGSK##)j!WcKe0NPu;hZgNrHHl#N^IyCp8Kj7
z=13GGStwd4c*!kn(xi6ortsM8T)VW$FX@+NOBT<nC9xdb9(F#W9J4*+DE<et6Yw<y
zlKwCo69Wtk@xPe;|HAcZ-`d}}{wH(NivNx4MoqmxxW@D*sre8(G_t8(N}-~Q{@N;j
zj676B_4du59}!Aer9n1{94kSZ{G*Zol;(`-RGB1Ycf<l=j>%t4KgZMge2Z-7<Ne9?
z>Y4@XFvqetS=VE>_JWMMJOU(}qHp`P5aD7klEhaNH`}=PXRt#cr*vuG_FEk(E(|fN
zl?h3h`Pt)Hsfhis1j|-|kiz8mLJr_$90G~LV7_lmP6(S|L>UPn$2|@@Upx^qlTR+3
zF^-Z}$D?{VWVc6M7&WDK>^kktx?<2MWLPi0&SM!y&oo2^W%@T`yWqO#w=cQ^oxuU=
z?5OqEQ$>2jH$ix-KGxF24kOV<EF}T)o}XrgRPE$cWJ|Qh%7g7BK}K9=eY?y-jlopv
z2V<hyEU#T=KZ*T1glmv+QY=mBrxh7*srJwjs4-ggJaF{2G;eqUEfaL0%n&4OvH`Kn
z!e+6myT5o#G970Wp50jjsyU{!@RA&!EsxYL`VF^e%f9#0)|z2!?DNx8Su4qdV;HHm
znS$oU4D<cgB2*a3T7y^~t?)32nE1<0KV%F?eymK+q?5#y?bVQb$SD(7CN0~LP0h};
zks^nw1zk5M1<blI4$ZW}YjlqjpzI|;pu5bnO^vAwA6PYvo-l&P3^HK?mjVJJAVNZ(
znGtK6N5dP=B>9<h05%{snT)9rokfD-Fc;}iy)TcyqHM^OAqqg>3rbr!FS=c{g#wGV
zkPQt>ovC?8LM1b-3)$tvS(dQz6rHPzwk5QnuKig#q?D=8u3(||io6CdTQohshN73%
z8&w2t%8#W<l_U<(2>{aNv7YT;klX3tT4|=ZMp*%1b(q>u5^9Y8)k7zvlJ#P2Dm}^}
zhbf0a$xe9ry2bBHD823s>hOKtyIfKGlP|_x5tuIV0q%3688L;HsKg`3OE9iUY)ety
z`tt)b_vK#@T@3A^)7h%FfA3jIlz#VL45zNm47uv8_U(9H8gLyHbn!S{K`88Bex?s(
zf{}uc`?{ox9Ab~#=)m$KT*mE?Q-s94(}3m0NgI~w=!*vFbRz5O8TeMfd#(p+jL1Zb
zgPah8tb=c#AF-)?CbXQ4$?RZwz+XHW&aZVT(YAB8v#*(9Xc9sdo06vVQ7xtoRt?8y
zbzV1Ie`1{~S0=3;o2M&IoCs%_PWC5^WbTTi0F7mwllmLDH+kkrba<{3F*xHoCyMSM
zQK6%Gq~3VU;njY!_I`UYqbr`lhE+5;P1E<l{4x!HN^2|XR4&`OdO5=X`*Ea}m08U-
z-}IuZB*x4-;Qood9(7Y1Ce#Ym8bwA9>>!96d#;S~(6YKbT59}gq1HC!g3p<+_Dg^I
z4Z;%S8M$eMQ&rbub&ea;>(#3<3pe_cjeRA&EwMLETjoX7!+vS2?y>>h)J5>q?#UK*
zqCYh8tw!82WU)?DXL`qXXb<bSgaWQ}{PCP+lDR>YU2$1@%Zn;J|C`(*$nQ`16HyEk
z90ndb)@(PUrZZy#HFugvrs$8tevEe2cGCvZz5z1woaGAB8)cj6Mnm}ue3*3FJP`6f
zTq!(=t4i7M$0TtMjMy{8RhqX4m6$W^IC1hP1Msw9CcI2+w{lV`_w<VGIuXc=>)LfP
z685O+2l-6bxOb7U$62?22^jXy`_!LK-#5P?9%E@-@K$!9Te2KEfM_(8Tx~*m)yQ9L
z^t)=5xQB|CTe=u?o@a;9BD;TIV!g~pKjNh=7L#m({X)27XhCM8=(0V>bE)(oxvzR8
zL!ML!7woNHmbxT*9m(B3vOFx`^nW`Hx)ge+9R@!S#ORWwdZinD>xbL&e^L2d?+<gX
zFuejz+>D|Celcahd#unS7mPfXE0V&&gX$|{?)Pw{Q5fir!o%_E>2tZ0@M2~?^JaO{
z|M8#HKjD*}FvSJ~E4~5)L;5f31O8vw2gg|d8~gv{U?%<l`AgS3`LQxm_ug5tz$<&T
zlhr=@l`^V3i?X$*n<c#4rHd}y)ulX$-OpIBh7zy?5L|wDAU<mANspWw$M=sTG!mV!
z_*s{BbaYf*+FDx5@!a|GdeQ33XYr*uu%sCG`Q;N(haRj<CgkT~??Z4n|57>j`_<N@
z;CeWQRxQ*#E_{j6lA&Q*h6RGHWX{GOLKzX*g{f$Ug(5IG-XdB6vsLFH`FwfuZARbH
z)W>^i_E~bUZl!hie4}#}p^0jZ#r^pprQ}}zF>u7SQKu?*?ehBZ{JSOm#V;PUxp`~J
z7SL<F;2R30*hbc;6Z48MJcxB|qh~1*FucWY#vppEC-BGB?)Qm!<BxVQfOuelS>y^X
z2gCI%^5EH}ZY<rrbZDcpL#bvJR(uULHv0z7aqbE)&Y<9Nf#o4oC`4bcSSnI?P~Db*
z2+G+Ju1}mqfk055A;HD{5QG7Q-rQ!WLBICmT+37w8hXkUoA{bCpzrZ?dX}kU0pmrF
z3tMiQbBtzg$DM9V_9(NUTxjOKhkanGp)^X~Rwv)=aBx5jn7e+4W}D-nQISmH6W9Vq
zGEl%M`V=UMJ(dQ}%j*}z0`<Ys@Bu^Wvm0&-F*o!n=9{05p9tvEc2Z$1`EcDazN4Nx
zBjg(+jY%#$Me$9GusxMR-<wEW(B6l<s+#aL44{f6E#yAMsC*v<51Zw)DuQE;C-gk8
zv9b(G)pLqg)7e0t0C#&Ezea55S5WR^lXIYKwY4)`a9;Ks(mqg|?q)e{qaSbqMYtM)
zsJ9m}IB9v-y%&?5EIewlOqr>!$dD+{YKMWALszL#mTgZd{Z$mB$_0-Dn4d4aFv2M7
zWEQmoTZ$n!2PHL!q!%xywmG`Jv>W-`$bY`x<dAuL5ORh_fnUFS$%xYwX}|v4&*0w4
z0%!`~&%GrAQQP4KD^po8JT_DfSZnU~(0BR#5iEPjL5!r}1w#WWK8F`!w0Y<*B5~@U
zP3P$^S@X?*leH-ZzSd-1Bz`|^MqYLZSz}33)~>Dj?mSoqF3IHwOB2sTl<lZqzt*`q
zarc%;@U*-2B6R%b{NwG)(-F&yHr0iWLKJI-YYcmwtbrlqn2_*XW2e?qkp~P2$yhrl
z&xUf3?dpn91tKQ0Sr3V9k}j;cQ}=cAR9OIO$MQR@;KlUa>_kpJe5ZMNsm!bB{~@g=
zZmZBoJRGzj7Ci&i*|5^UVoy-2-k*x=L#rlA7^SxRY{L~A&Xn^7+&5QD+u2^{%t=84
zB3N(_g+~R?C*>m6u5>;`b5g0YSvt0IF5<9rMnoHm1fWthD=Kr1pz1_`9Iq09<b3Gp
zwk@Z@DtjxrDwJ{n*9H>|O&A8-BZBn$G{__!+gxj?a@rA8!g#OtIag>pCk^!@ijb_p
z-^)maV0E_i?D1U#y8&O3wWL7<&c=|&K3-mLPAWAv&y1HyL2N!i!S~&txBlS7Q&(et
zD(%$v0JhmvrIt+jI=rkYixXB_5U$8PXADPkt>kMOeblt9*1$SA<$Bh$rX)B=NysgP
z!^Kv*zqlq=3J#Dwf~tl{js5r7H`{6Pz7;O_dTqro^)(7@;Mhc97H*Jvnm1-iqzMzE
z-%jn_m3Vts#>M~&9xRCm6M4Hd7Dm$;*C(Vdx$fo{ghZ>U;XkMSgs35mxlKk+$jx&_
zO(HXRK&PfQ;E{+3&lb9apC~|yM*5+fqR9L@3^pL&ZMPY$$rGi~v}P(DDG&sBbQC0}
zUD+-<#o6y~UqpNh1LxxMeH6|bFl3+UM?HID9{8-V+Daq+1`?G#HqpbgpFKauatA|9
znH;PS+m?W()UF)c7cj{KYrD@y?^ACJ)%%@mo7OKdnR2JUFB9_`zADDb3v773uJC08
z-r8)~2Mz3W_TEc*_rCa&g0w9mOe+A8oMCmT;f6L|hz%nka*cs&9Q>*ld-zGQe7+Pw
zzS1t_xu21{i4J5m(^lW8o!^tmc9Ex{A7a9V)=(hM<C~ki81NefitIEE3Qt$WP$6ZK
z^wo8kZM+0=T7d$wlOI<6U`Nel|0qR^IKI1Kgn;`L_;m`5M&ED3op~K2SjvuJW%R4W
zK5{tZ+Aplabj^H{)YEdx!;p!$qd|XfRi>F~?qn7vz)>Hi!Vwv(nFgq{3jX_0JWzHd
zD3hWsfnox!+&|i;E-Uyho|2lAxvydfvdYvv4ttd{S(aI<Q}z(Gk{qKUL5q{KL+VSq
zVS-Qk6q&j>wFMPhVB->XxoLpZvzbWfkPfwOe2vPW)hM!}@hZKgnKyfRIuc?X>kr|I
zQPwYxD@BP2C3tZNM5boD0duKDWqnOjG&r(sq&Pg^3Pix&D@|Og>CARqyhyVjBC+nY
zkF5gt6{t?ehz!cl?SB++FkQjSWCbbI&h5x><WxJn@HXpq$vv`XtWCDxL}s5G?NmI1
zu0=x%a!$`svYs)Yn@wlYqrf2?tY0rYYTq?tUmoU_-h{Z?trmIX-A^W4t47ZUXV0~6
zcCLo^45}tuzi;NkB+qbim8rjDEf;$!uI-^jhU)0(T){h>suCH;fbZerLZJ2&j2jNJ
ziLOFQOrAQ&Mk^k`akz7E#?xx!ln|+ur)0{`;t%|ANIf#WvU6-=X2T8l3WMwZ>>){@
zB?6C0go&MQ<&O=USU!CjGDcBfU|WEu7+b09RrzesOhcc01d%WSZ`~^#FqGS@zwUKv
zVBqz_cc{VSL9uID{ZRc7QnfQt`g8O#<#Ix|s^Mya;NlfKs3m2c+nhHPpjJEd9v%5;
zQ{2v$Q}I1EQhbnj#~sk-=;8f&QVO*y&DGpOlv@}%qFMjW0p*AIW0k%Ds*C}0<4b1d
zOGm!msdwwxGVe{}kKzFm>YIsftCti`PT3cPD*nsP1sGmfOXZXI1Co!TY=q8x>*y5}
z`XkTYwpxjS$H7;KH@&l3?|aoH{S;_{J9!z1T+Gs9e+7-yk}bg)SvknujbiEmls09I
zZW^)C(RtURgbY}Lz;AMpG-oOp-CF0E0e5>rvnt)x%=}nw;|^ti(ARl*LNo1B82PSd
zB=Z4BrK|eb?_GWL^g;*d74_vNnbg;&edU2|RA;{xR0<vF>mjmGk*OhNEh~6d{r2n;
zDN;6w1(>G4$Xc@;C1a!8E9eNN3j{Z2jclpYeUe4xBWPjx!V}4l{WzAe<t`9$hc1Kf
z+873@_oU_Tn#*DW_Ru7RG-m4Glf0)nyxZcp2p=~2aDWsxI-(7+jZkzA-DhT21%4%7
z><+PASC``_7W4=ryN*h|3+V$IjS!)y{;l4|{!!_Zf2$x$a*l*tSCpH&^|(iLIgse~
z^<Qen<sX%h_qWQ46Dv+~yuC0oUm(OZ2odmA)cs3s_)EU$HIKDD-bra~b_;+@J4Z|Y
z%sZ(=q-Q;kVI^2{EhT2eCZ!?hJdsHHdCOyuI-q*78){O{zS3icc}ofpw?-h7olx1)
z;*<v2g5PG}2ef!ih8ZQ!0Wi&PjNUOVZpg^}38O{SryqP5KuT~XnZ`e%wC+!Uh*J%j
zyswl&zjV>~6Yf9#3FM1?B3{_$3^Lu3a4E%`+|1hiH8mg?CdLdC*L6WQ-l&&I<Z91$
zAJ2jZyS}<#O>_IMS2wqnYd(CBIlfdH>AIfvUQ~+)@NKzki~Kj_&ZDf9P*TaiYh!y*
ze2JiGd-F8%f#N#&!poq>)f*AmiX1fex5M8)8Z8pOvMWF%Cqx3YysCh=L~NI^x>Maz
zUYC%3jr~ehc|@EJ13vmXeKP71`CFZgG*`tg(gDvoo_+s0;rD3NciyxskrT#KG)QDY
zc{!6XFKl3bhmEkQ)1Xx!ys?B$WL1+Y3sZ+Z8g1*be%6K;Ze<Afi@iTD{u?#ay3T9K
zBd5z7D^*iou@n{SK`%1f@%la36Y@{DKFY1pr}eNQK8lwg#+g;h4V(-w9HS@cCd2yX
zNDzl1NO6sFp2?<t$0b{+(Ya~QrvtLnmmt9xF1_9TL63+1;{v|s6W0!@gWujamnJ(Z
zmR?SVKZSNxSE`fI7rG{WMQz?wov+_;WlXCrs)zBrBx8#R7{xqQ2R~=y_4X|{Xbst=
zX6HXBiFG2x3&xIc(F;W?8lhh@RrGgqh<-$+BsfCUKA!RlIhIIvqGR^ErjTfly@@Ii
zc#q2(q`oQ7L|9zF``FtSw%Mt=C(5lW?L(QT-xg+9t-h%cUvC2y9t>jdJ2r?_JJmB5
zde;XFjXSnbG^&y#8ja1F4rlqg;RpH0P*TJW5LhD!tmwzvaTtV5Q?z3CIaY@eyR}v(
z=uzgkV{8IdJHDAEn`t^H>AU{EBItz<R?|Skpr=Fx|1~djRJZo(WpK1$hhJFnT>JZV
z<-_O6LK_qc=GCaqXqFAG#SZI6v=R1T(tew|vC|3D*4HG!hI9Qa1gjl{6F_;<etg{B
zgLN|)WqaOie2oH_jm=RH5%iU3s*Z~Fq;U5te*iWSH|LV@=Dv?`<3uw!K%EWN)%Dd+
zju^YQZzJK+TJ`umP<=Ja7ygELG{lq`8_pQi7ZI9>Cz>p`*$HWn=L_+A*PQ|dZz*8z
zQ|DX9!PUwAc6}$^%9ERtaqvKOzQX=6VS5ei+QZM);)z;+m0a>tq^DOB<}7-=aCaWI
zaeF*w<CFB`3G_E2r_EGMDm9dVB^ALy8W(`LNutSg57m^R9|~a&O5t}+GGxnV5NN;}
z4Y;m_@8@;E)tMp2F>@%_VBbT8(JzAAMzjdxARTu@fYOow*>84jJb2N=GNIn`79)0K
zZn4cPCN-a&FOFraD7eVtG{i@eehAN4fGSUuQHGFEM$keYUeT4>UptHg>UCO=<GXV!
zh9U@CMwJf||1?kj`qRY)p!KM!m;04Ut184I(tBDuVVUPV2R5vxDsRvDP3S%Fg<W`}
z)K$q2_8MRV$4QBODVh3QLSjT|4!hNX8>jc0n#GAVpo+PVQbz&Cd|%w7?-Wrz5;1lI
z-4JJ;(=($kawDuv!+Ls~S3ZB@K<vjv<AgG->!;!);p3Y2DVyl_n~IYXR2VSMY-@Dx
z7v>^PTT{U#xlI|$nNpAJ&?!*5WRtAKPkIRsT)o&$Z2_0*%1EirSYy?vX%s0`Cq8UE
zWyy!y8bE}Mr$M<<!wt~gtYM*ScILK6JQ=;<ane1@QeTZr2KO;Qp}9Yx)y=D&nu(_p
zXOUi%5J8m#g_gt#3}fL2a%Lh0bt(u+eA3h&rS4GQ0P4$&t+@nu5mGIUoxMRJ%UNvg
zu7>yU3H8`zx?<V<>=AMVKf^JUJu-5lY1=^^zeV8YB3qdtfJ4O01Pu#N(6^Pt(q&^e
zRI$0iEZZ4fab!V=%Iz4}&P8&=PrKki>4i0trXYWXl)ZoP2kkW9a$g3+nTbb;&z$UW
zV8=zcQdf8Y$|?dhgjGWK?ML(%ys9u-gFGo3>e+>=J&*hxX{fb<QT4{LCM#omI6^(l
zj$0BpHw5QD-IHtTErM3uB~-XLoen;SWbc5b^?YLw6=;n?st_XKxv;rWSRD(|!(!QM
zpgYHwDeg@h=*yNF(jJ4oNEr!Dril|D@6qK)<i(;FLn06P<ofdZDap}`0^DE;+SKO}
zg@^mLFB{TQ#9Xn9ZOP*N*wWV0VSEo|6plT0mBG==(u@O$Iit%Cs@b2xGc5vD?l~No
zmbDSfCyay}pdwpTf5)RvE}U;1Py1YsntWpKvkYBKuUjc-!Vy`kOI>Tgk(-NtJqO~U
z2gEtYQBeURw?<eT_L_w2AT>Ve>XgZ`7i2k}%fM`qO78~ui6<aC)?~5PX4wY5bK-tS
zq6vvF`Yb{!PaC#gb`oQvA<AY=@TJcDxWEEA%>r2;Yy{6yRu%?xwi{aU(`QBr9+rNx
zU+g?eafD-RwUZN~n@P$qEK9;uL6X9_D*?<oAkb3M9Ef(Oa0V5PP~>{}hjJvYRW%~M
zrlRvXU*U!v(s6Lp!?)Jv#Jq@rRXf>cT6Smd{2cZ?t4OjWnNQ0kedUAc7QyVwiqjOo
zufCSUyhm9na!VJ*<a~iNhyHkib~ZjrB^eqQ<Tv%0o<y%ljsh$jSF*W8_LptUw!{1L
zgM+GJx)1De8E00r=PeAOIlFkeny|e6adfu7Fv_F{hPx>@goi}dXkGxhs8a15Xzq;d
zXvD$yQpTw(x4%8PC=V}lRoR2)>_RR?;%&EI0nL+`u3e>bwYHosi+&PNT93=5n_+IS
zhZwIHT_E%rx6NgF?YV3WlM49mkoVvZXtkn06-KG!cbqA->e?wE+0DSny^ZZ){(Hhz
zq_cQ3!JB@rYvdP`zOB{!AsP&|GwE&e;b$$Ce8x3-%;%^G)`>4;9{eYieI#51E;bFv
z%YB;`K}38(jyuI)QK!lhY9>g~U<hnTSElL^lNV6GQ4IM!8T;%BbwBxmGdpp7xl6&;
zOI0#NlV1*oB$H4tqi5DI)zT9^Yx6O{O4n<U5zs}m2(NdmXUgpCyY?vo%P)OMgHxVA
z_}m5k(zj$l`Z}Pf3=N;;eRy2wFewnTXDw#~kW?#eL)`VDMq4L-50d){9+VsHJ(#h1
z8oyFtHt(#IEl|+x1zvh)r+|I`8(r930j`rA@EJBJwFbVPKQAOioJ^1?_2?m1PoMKV
zw+u#DCV{%-Gt1~Gb_M>JxhKgdpq!BNk_qqYSJ0?|Z7pvo@{s+Cgp=NVJ=Dw3+3ozd
zn_ujrx2)?Vv0wv=ZQUDbWYuG}5MDil5_IH^J>2zD^($<{Lm>>@!YQDk4P$antPH!Q
z;>nRLPI>R0xkX~RL94IMD)ACrNccdE%+w;wF8{Fm0j9$|HLtu_;ULCdKpelzx-68l
z1nS`FlBis;I6H)xv(2(%X7pONm3N@m=U?{E8^Ja%FD*6}IL%3#z;=V*%E!IODzXM2
zq`|Vsr5K;dET<a#JK!A_NSBbqH4xNPcfwn?FR25_6<OUK4ly-J)E&Ax($l}zM)Ooh
z@sN}%9V|zJJKjA#&L7@f@p)5UAh^MMw<#UYD<4kSDIHE!Djmv;1fK&iJsL5e+u|hh
zapn$gGzurh2y34S6%TIy*rf54)=k<eWFKT4;3yp|c3ypavZ188Eh@E;pK&=C*LJ|t
z8fJ9Slr_>N9!~C%_tv|;)0U@Ir?wL|^#Wmc1hOJ4eq4y?Eh1$Sa(~_Q^X~ZpIHZ)5
z)}|f-vS-nGLi~7;pu#bRDz83d(6sEs_s&+cU!f=dROA)p+02||vx`7YSot`UP^M$9
z(j{J91WzVGw=iHKWU=M!f1>`nV`qri9fm@@9mDO#yh8y`AVA3%D(g={98bC=TKFs6
zn^!rCiK$*c&K&{OfZzl>?XHs5R=90prHKK2yCSU#7LyGKV8TcZHHtb#?Yb73LsFUR
zi<B}@`#GIlUc{wFuzbH%ads9>RPa#KX`R-~@3lu+=DMnPIS(@WF$sFApe-L+DoFLc
zDDIm9%_JZr{p!f7om`z^%QzIJNPHQUzfj&L01ke)I;mmvnmX^u)svAt=oJ@W-}a1n
zzX!4)^}b*JDPx0wVgUQUjhs;a@6nR~nJ5AKKL=3$e}+x|`-=bUkpBCMhChANf6uu5
z+x?%O=s)?N-spe3|7Rus-|iI%|LG3+xBWl0_kZ#~HF!lCDCoaF0>qz}6dVl9f&8!4
F{{mS)ea-*?

literal 0
HcmV?d00001


From 0659a9cad4b7cf68a2dbfdca2f1e660a14f07f8e Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@users.noreply.github.com>
Date: Mon, 24 Jul 2023 22:26:51 -0700
Subject: [PATCH 14/41] Update test.yml

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 3bd8cde..b4acccf 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -41,7 +41,7 @@ jobs:
       run: |
         REMOTE=/app/nf-encyclopedia
         docker run -v $(pwd):${REMOTE} nf-encyclopedia:latest \
-          pytest tests/unit_tests # -w ${REMOTE}
+          pytest ${REMOTE}/tests/unit_tests  
 
     - name: Run System Tests
       run: |

From 2b9ea7c5c120c978a1b4791d9354a1f4672adc4e Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Tue, 25 Jul 2023 14:17:01 -0700
Subject: [PATCH 15/41] bumped ims conversion version

---
 modules/ims.nf               |  2 +-
 subworkflows/encyclopedia.nf | 42 ++++++++++++++++++------------------
 2 files changed, 22 insertions(+), 22 deletions(-)

diff --git a/modules/ims.nf b/modules/ims.nf
index a537c9a..7e840cf 100644
--- a/modules/ims.nf
+++ b/modules/ims.nf
@@ -2,7 +2,7 @@
 process ADD_IMS_INFO {
     publishDir "${params.result_dir}/${group}/blib", pattern: '*.ims.blib', failOnError: true
     label 'process_medium'
-    container 'ghcr.io/talusbio/flimsay:v0.2.0'
+    container 'ghcr.io/talusbio/flimsay:v0.4.0'
 
     input:
         val group
diff --git a/subworkflows/encyclopedia.nf b/subworkflows/encyclopedia.nf
index 9f7f15f..5a4889a 100644
--- a/subworkflows/encyclopedia.nf
+++ b/subworkflows/encyclopedia.nf
@@ -62,8 +62,8 @@ workflow PERFORM_QUANT {
         quant_files
         | transpose()
         | multiMap { qit ->
-        mzml: tuple qit[0], qit[1]
-        elib: qit[2]
+            mzml: tuple qit[0], qit[1]
+            elib: qit[2]
         }
         | set { ungrouped_files }
 
@@ -86,26 +86,26 @@ workflow PERFORM_QUANT {
 
         // Only run group-wise global if needed.
         if ( local_only ) {
-        Channel.empty() | set { global_files }
-        Channel.empty() | set { msstats_files }
-        Channel.empty() | set { global_blib }
+            Channel.empty() | set { global_files }
+            Channel.empty() | set { msstats_files }
+            Channel.empty() | set { global_blib }
         } else {
-        // Do the global analysis
-        // Output is [group, peptides_txt, proteins_txt]
-        ENCYCLOPEDIA_AGGREGATE(
-                local_files,
-                dlib,
-                fasta,
-                params.encyclopedia.quant_suffix,
-                true  // Align RTs
-            )
-            | set { agg_outs }
-
-        agg_outs.lib |
-            map { libe -> libe[1] } |
-            set { global_blib }
-        agg_outs.quant
-            | set { global_files }
+            // Do the global analysis
+            // Output is [group, peptides_txt, proteins_txt]
+            ENCYCLOPEDIA_AGGREGATE(
+                    local_files,
+                    dlib,
+                    fasta,
+                    params.encyclopedia.quant_suffix,
+                    true  // Align RTs
+                )
+                | set { agg_outs }
+
+            agg_outs.lib |
+                map { libe -> libe[1] } |
+                set { global_blib }
+            agg_outs.quant
+                | set { global_files }
         }
 
     emit:

From 5f74e08026bb381c6287a2c7085628b18338da2f Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Tue, 25 Jul 2023 14:24:56 -0700
Subject: [PATCH 16/41] updated msstats tests for resolutoin

---
 tests/unit_tests/test_msstats.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/tests/unit_tests/test_msstats.py b/tests/unit_tests/test_msstats.py
index 0a34bbd..2b18186 100644
--- a/tests/unit_tests/test_msstats.py
+++ b/tests/unit_tests/test_msstats.py
@@ -15,6 +15,9 @@
     Path("QCPlot.pdf"),
 ]
 
+"""
+Note that the script fixture is defined at the bottom of this file.
+"""
 
 def test_joins(msstats_input, script):
     """Test that the joins are made correctly"""
@@ -217,7 +220,8 @@ def script(monkeypatch, tmp_path):
     """Set the working directory"""
     (tmp_path / "msstats").mkdir(exist_ok=True)
     (tmp_path / "results").mkdir(exist_ok=True)
-    script_path = Path("bin/msstats.R").resolve()
+    script_location = Path(__file__).parent / "../../bin"
+    script_path = (script_location / "msstats.R").resolve()
     monkeypatch.syspath_prepend(script_path)
     monkeypatch.chdir(tmp_path)
     return script_path

From e6f583266c7076be2d3dc0d20087ec8d1c0ea3b6 Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Tue, 25 Jul 2023 14:32:44 -0700
Subject: [PATCH 17/41] fixed input piping to ims

---
 subworkflows/encyclopedia.nf | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/subworkflows/encyclopedia.nf b/subworkflows/encyclopedia.nf
index 5a4889a..dae9a65 100644
--- a/subworkflows/encyclopedia.nf
+++ b/subworkflows/encyclopedia.nf
@@ -91,7 +91,10 @@ workflow PERFORM_QUANT {
             Channel.empty() | set { global_blib }
         } else {
             // Do the global analysis
-            // Output is [group, peptides_txt, proteins_txt]
+            // Output is [
+            //     lib: [group, elib, blib, log, summary.csv]
+            //     quant: [group, peptides_txt, proteins_txt]
+            // ]
             ENCYCLOPEDIA_AGGREGATE(
                     local_files,
                     dlib,
@@ -102,7 +105,7 @@ workflow PERFORM_QUANT {
                 | set { agg_outs }
 
             agg_outs.lib |
-                map { libe -> libe[1] } |
+                map { libe -> libe[2] } |
                 set { global_blib }
             agg_outs.quant
                 | set { global_files }

From 61c6b0ea1824512b524e462eb9196e089b0c047d Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Tue, 25 Jul 2023 14:47:33 -0700
Subject: [PATCH 18/41] changed log handling in skyline steps

---
 modules/skyline.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/skyline.nf b/modules/skyline.nf
index 9747e2b..318acb5 100644
--- a/modules/skyline.nf
+++ b/modules/skyline.nf
@@ -60,8 +60,8 @@ process SKYLINE_IMPORT_DATA {
     wine SkylineCmd \
         --in="${skyline_zipfile.baseName}" \
         --import-no-join \
-        --log-file="${raw_file.baseName}.log" \
         --import-file="${raw_file}" \
+        2>&1 | tee  "${raw_file.baseName}.log"
     """
 
     stub:
@@ -95,12 +95,12 @@ process SKYLINE_MERGE_RESULTS {
 
     wine SkylineCmd \
         --in="${skyline_zipfile.baseName}" \
-        --log-file="skyline-merge.log" \
         ${import_files_params} \
         --out="final.sky" \
         --save \
         --share-zip="final.sky.zip" \
-        --share-type="complete"
+        --share-type="complete" \
+        2>&1 | tee  "skyline-merge.log"
     """
 
     stub:

From 427ff6316fad884d3a2361d16a2b6c00d02bf788 Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Tue, 25 Jul 2023 14:59:42 -0700
Subject: [PATCH 19/41] changed log handling in skylines first step

---
 modules/skyline.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/skyline.nf b/modules/skyline.nf
index 318acb5..1bc5c8c 100644
--- a/modules/skyline.nf
+++ b/modules/skyline.nf
@@ -19,13 +19,13 @@ process SKYLINE_ADD_LIB {
 
     wine SkylineCmd \
         --in="${skyline_template_zipfile.baseName}" \
-        --log-file=skyline_add_library.log \
         --import-fasta="${fasta}" \
         --add-library-path="${blib}" \
         --out="results.sky" \
         --save \
         --share-zip="results.sky.zip" \
-        --share-type="complete"
+        --share-type="complete" \
+        2>&1 | tee skyline_add_library.log \
     """
 
     stub:

From 17c34a60534a958596a04489a72f8dc5bf51fb58 Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Tue, 25 Jul 2023 15:18:05 -0700
Subject: [PATCH 20/41] updated position in skyline adds

---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 93947e6..470fb06 100644
--- a/main.nf
+++ b/main.nf
@@ -132,7 +132,7 @@ workflow {
     ADD_IMS_INFO(groups, quant_results.blib)
     | set { blib }
 
-    SKYLINE_ADD_LIB(skyline_empty_template, blib, fasta)
+    SKYLINE_ADD_LIB(skyline_empty_template, fasta, blib)
     | set { skyline_template_zipfile }
 
     // This will generate a skyd for every raw data file

From f9baf4ad6889f149a04de8ea733eecbdc2296ba2 Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Tue, 25 Jul 2023 15:45:38 -0700
Subject: [PATCH 21/41] handled decompression

---
 modules/skyline.nf | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/modules/skyline.nf b/modules/skyline.nf
index 1bc5c8c..a31d13a 100644
--- a/modules/skyline.nf
+++ b/modules/skyline.nf
@@ -56,11 +56,17 @@ process SKYLINE_IMPORT_DATA {
     script:
     """
     unzip ${skyline_zipfile}
+    if [[ ${raw_file} == *.tar.d ]] ; then
+        tar -xvf ${raw_file}
+        raw_file=$(ls *.d)
+    else
+        local_rawfile=${raw_file}
+    fi
 
     wine SkylineCmd \
         --in="${skyline_zipfile.baseName}" \
         --import-no-join \
-        --import-file="${raw_file}" \
+        --import-file="${local_rawfile}" \
         2>&1 | tee  "${raw_file.baseName}.log"
     """
 

From 777f65fd63273d25dc583c9bbcb30c4b034031ee Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Tue, 25 Jul 2023 15:53:59 -0700
Subject: [PATCH 22/41] handled decompression on grouping stage

---
 modules/skyline.nf | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/modules/skyline.nf b/modules/skyline.nf
index a31d13a..269636e 100644
--- a/modules/skyline.nf
+++ b/modules/skyline.nf
@@ -95,9 +95,18 @@ process SKYLINE_MERGE_RESULTS {
         path("skyline-merge.log"), emit: log
 
     script:
-    import_files_params = "--import-file=${(mzml_files as List).collect{ "/tmp/" + file(it).name }.join(' --import-file=')}"
     """
     unzip ${skyline_zipfile}
+    for f in *.tar.d ]] ; do
+        tar -xvf ${f}
+    done
+
+    local_files=$(ls *.raw *.mzml *.mzML)
+    import_files_params=""
+    for f in $local_files ; do
+        import_files_params=" ${import_files_params} --import-file=${f}"
+    done
+
 
     wine SkylineCmd \
         --in="${skyline_zipfile.baseName}" \

From 9529b39ffb8128ca4f037b25c24f7b04dc899e86 Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Tue, 25 Jul 2023 16:05:38 -0700
Subject: [PATCH 23/41] escaped bash variables

---
 modules/skyline.nf | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/modules/skyline.nf b/modules/skyline.nf
index 269636e..aef810f 100644
--- a/modules/skyline.nf
+++ b/modules/skyline.nf
@@ -58,7 +58,7 @@ process SKYLINE_IMPORT_DATA {
     unzip ${skyline_zipfile}
     if [[ ${raw_file} == *.tar.d ]] ; then
         tar -xvf ${raw_file}
-        raw_file=$(ls *.d)
+        raw_file=\$(ls *.d)
     else
         local_rawfile=${raw_file}
     fi
@@ -66,7 +66,7 @@ process SKYLINE_IMPORT_DATA {
     wine SkylineCmd \
         --in="${skyline_zipfile.baseName}" \
         --import-no-join \
-        --import-file="${local_rawfile}" \
+        --import-file="\${local_rawfile}" \
         2>&1 | tee  "${raw_file.baseName}.log"
     """
 
@@ -98,19 +98,19 @@ process SKYLINE_MERGE_RESULTS {
     """
     unzip ${skyline_zipfile}
     for f in *.tar.d ]] ; do
-        tar -xvf ${f}
+        tar -xvf \${f}
     done
 
-    local_files=$(ls *.raw *.mzml *.mzML)
+    local_files=\$(ls *.raw *.mzml *.mzML)
     import_files_params=""
-    for f in $local_files ; do
-        import_files_params=" ${import_files_params} --import-file=${f}"
+    for f in \$local_files ; do
+        import_files_params=" \${import_files_params} --import-file=\${f}"
     done
 
 
     wine SkylineCmd \
         --in="${skyline_zipfile.baseName}" \
-        ${import_files_params} \
+        \${import_files_params} \
         --out="final.sky" \
         --save \
         --share-zip="final.sky.zip" \

From ea299370b17130618df991047562dbf0d387b2ad Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Tue, 25 Jul 2023 16:16:42 -0700
Subject: [PATCH 24/41] bugfix minor typo on file type

---
 modules/skyline.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/skyline.nf b/modules/skyline.nf
index aef810f..f871e15 100644
--- a/modules/skyline.nf
+++ b/modules/skyline.nf
@@ -56,7 +56,7 @@ process SKYLINE_IMPORT_DATA {
     script:
     """
     unzip ${skyline_zipfile}
-    if [[ ${raw_file} == *.tar.d ]] ; then
+    if [[ ${raw_file} == *.d.tar ]] ; then
         tar -xvf ${raw_file}
         raw_file=\$(ls *.d)
     else

From 88b9d496e2de65d52178c013c414992a2047b81c Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Tue, 25 Jul 2023 16:26:47 -0700
Subject: [PATCH 25/41] bugfix minor typo on file type

---
 modules/skyline.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/skyline.nf b/modules/skyline.nf
index f871e15..f037baa 100644
--- a/modules/skyline.nf
+++ b/modules/skyline.nf
@@ -58,7 +58,7 @@ process SKYLINE_IMPORT_DATA {
     unzip ${skyline_zipfile}
     if [[ ${raw_file} == *.d.tar ]] ; then
         tar -xvf ${raw_file}
-        raw_file=\$(ls *.d)
+        local_rawfile=\$(ls *.d)
     else
         local_rawfile=${raw_file}
     fi

From 1241330f229f53654cf887c5c99a3d693ac41bf4 Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Tue, 25 Jul 2023 21:41:11 -0700
Subject: [PATCH 26/41] changed way to list files in bash

---
 modules/skyline.nf | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/modules/skyline.nf b/modules/skyline.nf
index f037baa..7776a8a 100644
--- a/modules/skyline.nf
+++ b/modules/skyline.nf
@@ -58,7 +58,7 @@ process SKYLINE_IMPORT_DATA {
     unzip ${skyline_zipfile}
     if [[ ${raw_file} == *.d.tar ]] ; then
         tar -xvf ${raw_file}
-        local_rawfile=\$(ls *.d)
+        local_rawfile=\$(find \${PWD} -d -name "*.d")
     else
         local_rawfile=${raw_file}
     fi
@@ -101,9 +101,8 @@ process SKYLINE_MERGE_RESULTS {
         tar -xvf \${f}
     done
 
-    local_files=\$(ls *.raw *.mzml *.mzML)
     import_files_params=""
-    for f in \$local_files ; do
+    for f in *.{d,mzml,mzML} ; do
         import_files_params=" \${import_files_params} --import-file=\${f}"
     done
 

From ca9ecc7ba29b07554839540e72ec486c8f43e30e Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Tue, 25 Jul 2023 22:11:45 -0700
Subject: [PATCH 27/41] fixed yet another bug in the bash side of the workflow

---
 modules/skyline.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/skyline.nf b/modules/skyline.nf
index 7776a8a..ec077f2 100644
--- a/modules/skyline.nf
+++ b/modules/skyline.nf
@@ -97,7 +97,7 @@ process SKYLINE_MERGE_RESULTS {
     script:
     """
     unzip ${skyline_zipfile}
-    for f in *.tar.d ]] ; do
+    for f in *.d.tar ; do
         tar -xvf \${f}
     done
 

From 585b568c92de768147de2e1328111f3acfafdf49 Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Tue, 25 Jul 2023 22:37:01 -0700
Subject: [PATCH 28/41] changed val to path in skyline step

---
 main.nf            | 7 ++-----
 modules/skyline.nf | 2 +-
 2 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/main.nf b/main.nf
index 470fb06..679b198 100644
--- a/main.nf
+++ b/main.nf
@@ -142,13 +142,10 @@ workflow {
     )
     | set { skyline_import_results }
 
-    raw_quant_files = raw_quant_files.collect()
-    skyd_files = skyline_import_results.skyd_file.collect()
-
     SKYLINE_MERGE_RESULTS(
         skyline_template_zipfile.skyline_zipfile,
-        skyd_files,
-        raw_quant_files,
+        skyd_files.collect(),
+        raw_quant_files.collect(),
     )
     | set { skyline_merge_results }
 
diff --git a/modules/skyline.nf b/modules/skyline.nf
index ec077f2..7446062 100644
--- a/modules/skyline.nf
+++ b/modules/skyline.nf
@@ -88,7 +88,7 @@ process SKYLINE_MERGE_RESULTS {
     input:
         path skyline_zipfile
         path '*.skyd'
-        val raw_files
+        path raw_files
 
     output:
         path("final.sky.zip"), emit: final_skyline_zipfile

From 4c7d79f72d97e544ec7ca8f2decb0d03fad429ba Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Tue, 25 Jul 2023 23:20:15 -0700
Subject: [PATCH 29/41] added debugging prints

---
 modules/skyline.nf | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/modules/skyline.nf b/modules/skyline.nf
index 7446062..a524306 100644
--- a/modules/skyline.nf
+++ b/modules/skyline.nf
@@ -96,6 +96,12 @@ process SKYLINE_MERGE_RESULTS {
 
     script:
     """
+
+    echo ${raw_files}
+
+    echo "Directory status >>>>"
+    ls -lctha # For debugging ...
+
     unzip ${skyline_zipfile}
     for f in *.d.tar ; do
         tar -xvf \${f}
@@ -106,6 +112,8 @@ process SKYLINE_MERGE_RESULTS {
         import_files_params=" \${import_files_params} --import-file=\${f}"
     done
 
+    echo "Import file params >>>"
+    echo \${import_files_params}
 
     wine SkylineCmd \
         --in="${skyline_zipfile.baseName}" \

From efd04ef79c3ff8dc86d56c61d7de048f84070ac6 Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Tue, 25 Jul 2023 23:28:24 -0700
Subject: [PATCH 30/41] yet another fix

---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 679b198..11a73d3 100644
--- a/main.nf
+++ b/main.nf
@@ -144,7 +144,7 @@ workflow {
 
     SKYLINE_MERGE_RESULTS(
         skyline_template_zipfile.skyline_zipfile,
-        skyd_files.collect(),
+        skyline_import_results.skyd_file.collect(),
         raw_quant_files.collect(),
     )
     | set { skyline_merge_results }

From 829081b785a9f7eab220cb395e940e78e545186d Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Wed, 26 Jul 2023 00:28:25 -0700
Subject: [PATCH 31/41] added more debugging info and added handling of raw
 files

---
 modules/skyline.nf | 28 +++++++++++++++++++++++-----
 1 file changed, 23 insertions(+), 5 deletions(-)

diff --git a/modules/skyline.nf b/modules/skyline.nf
index a524306..d202119 100644
--- a/modules/skyline.nf
+++ b/modules/skyline.nf
@@ -97,19 +97,37 @@ process SKYLINE_MERGE_RESULTS {
     script:
     """
 
+    echo "Input Raw files"
     echo ${raw_files}
 
     echo "Directory status >>>>"
     ls -lctha # For debugging ...
 
+    echo "Unzipping skyline template file"
     unzip ${skyline_zipfile}
-    for f in *.d.tar ; do
-        tar -xvf \${f}
-    done
 
     import_files_params=""
-    for f in *.{d,mzml,mzML} ; do
-        import_files_params=" \${import_files_params} --import-file=\${f}"
+
+    if [[ \$(find \${PWD} -type d -name "*.d") ]] ; then
+        for f in *.d.tar ; do
+            echo "Decompressing \${f}"
+            tar -xvf \${f}
+        done
+
+        for f in *.d ; do
+            import_files_params=" \${import_files_params} --import-file=\${f}"
+        done
+    else
+    fi
+
+    echo "Import file params >>>"
+    echo \${import_files_params}
+
+    for ftype in raw mzml mzML; do
+        echo ">>> Looking for \${ftype} files"
+        for f in \$(find \${PWD} -type d -name "*.\${ftype}"); do
+            import_files_params=" \${import_files_params} --import-file=\${f}"
+        done
     done
 
     echo "Import file params >>>"

From 5b76bfe23e078f6c0c605887bdaa8f25a50bed2e Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Wed, 26 Jul 2023 00:41:48 -0700
Subject: [PATCH 32/41] handled empty else clause

---
 modules/skyline.nf | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/modules/skyline.nf b/modules/skyline.nf
index d202119..1401861 100644
--- a/modules/skyline.nf
+++ b/modules/skyline.nf
@@ -108,16 +108,19 @@ process SKYLINE_MERGE_RESULTS {
 
     import_files_params=""
 
-    if [[ \$(find \${PWD} -type d -name "*.d") ]] ; then
+    if [[ \$(find \${PWD} -type f -name "*.d.tar") ]] ; then
         for f in *.d.tar ; do
             echo "Decompressing \${f}"
             tar -xvf \${f}
         done
+    else
+        echo "No compressed .d files found"
+    fi
 
+    if [[ \$(find \${PWD} -type d -name "*.d") ]] ; then
         for f in *.d ; do
             import_files_params=" \${import_files_params} --import-file=\${f}"
         done
-    else
     fi
 
     echo "Import file params >>>"

From 362dadbda2366b1d564293998d5356c725a3fd75 Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Wed, 26 Jul 2023 09:22:59 -0700
Subject: [PATCH 33/41] added a lot of extra params

---
 modules/skyline.nf | 24 ++++++++++++++++++++++--
 1 file changed, 22 insertions(+), 2 deletions(-)

diff --git a/modules/skyline.nf b/modules/skyline.nf
index 1401861..435ef88 100644
--- a/modules/skyline.nf
+++ b/modules/skyline.nf
@@ -25,6 +25,17 @@ process SKYLINE_ADD_LIB {
         --save \
         --share-zip="results.sky.zip" \
         --share-type="complete" \
+        --tran-precursor-ion-charges="2, 3 ,4" \
+        --tran-product-ion-charges="1,2" \
+        --tran-product-ion-types="b, y, p" \
+        --tran-use-dia-exclusion \
+        --library-pick-product-ions="all_plus" \
+        --tran-product-start-ion="ion 2" \
+        --tran-product-end-ion="last ion - 2" \
+        --associate-protein-group-proteins \
+        --full-scan-product-res=10.0 \
+        --full-scan-product-analyzer=centroided \
+        --full-scan-acquisition-method="DIA" \
         2>&1 | tee skyline_add_library.log \
     """
 
@@ -59,8 +70,10 @@ process SKYLINE_IMPORT_DATA {
     if [[ ${raw_file} == *.d.tar ]] ; then
         tar -xvf ${raw_file}
         local_rawfile=\$(find \${PWD} -d -name "*.d")
+        import_extra_params=" --ims-library-res=30 --full-scan-isolation-scheme=\${local_rawfile}"
     else
         local_rawfile=${raw_file}
+        import_extra_params=" --full-scan-isolation-scheme=\${local_rawfile}"
     fi
 
     wine SkylineCmd \
@@ -96,7 +109,6 @@ process SKYLINE_MERGE_RESULTS {
 
     script:
     """
-
     echo "Input Raw files"
     echo ${raw_files}
 
@@ -107,6 +119,7 @@ process SKYLINE_MERGE_RESULTS {
     unzip ${skyline_zipfile}
 
     import_files_params=""
+    import_extra_params=""
 
     if [[ \$(find \${PWD} -type f -name "*.d.tar") ]] ; then
         for f in *.d.tar ; do
@@ -120,6 +133,7 @@ process SKYLINE_MERGE_RESULTS {
     if [[ \$(find \${PWD} -type d -name "*.d") ]] ; then
         for f in *.d ; do
             import_files_params=" \${import_files_params} --import-file=\${f}"
+            import_extra_params=" --ims-library-res=30 --full-scan-isolation-scheme=\${f}"
         done
     fi
 
@@ -128,7 +142,7 @@ process SKYLINE_MERGE_RESULTS {
 
     for ftype in raw mzml mzML; do
         echo ">>> Looking for \${ftype} files"
-        for f in \$(find \${PWD} -type d -name "*.\${ftype}"); do
+        for f in \$(find \${PWD} -type f -name "*.\${ftype}"); do
             import_files_params=" \${import_files_params} --import-file=\${f}"
         done
     done
@@ -143,7 +157,13 @@ process SKYLINE_MERGE_RESULTS {
         --save \
         --share-zip="final.sky.zip" \
         --share-type="complete" \
+        --reintegrate-model-name="reintegration_res" \
+        --reintegrate-create-model \
+        --full-scan-filter-tolerance=2 \
         2>&1 | tee  "skyline-merge.log"
+
+    echo "Directory status >>>>"
+    ls -lctha # For debugging ...
     """
 
     stub:

From b5cd217239158ba63b02a863e776761ee234a713 Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Wed, 26 Jul 2023 09:47:12 -0700
Subject: [PATCH 34/41] added unused parameter

---
 modules/skyline.nf | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/modules/skyline.nf b/modules/skyline.nf
index 435ef88..4f75ba2 100644
--- a/modules/skyline.nf
+++ b/modules/skyline.nf
@@ -80,6 +80,7 @@ process SKYLINE_IMPORT_DATA {
         --in="${skyline_zipfile.baseName}" \
         --import-no-join \
         --import-file="\${local_rawfile}" \
+        \${import_extra_params} \
         2>&1 | tee  "${raw_file.baseName}.log"
     """
 
@@ -160,6 +161,7 @@ process SKYLINE_MERGE_RESULTS {
         --reintegrate-model-name="reintegration_res" \
         --reintegrate-create-model \
         --full-scan-filter-tolerance=2 \
+        $\{import_extra_params} \
         2>&1 | tee  "skyline-merge.log"
 
     echo "Directory status >>>>"

From 39bfc359070c7cd37bac3f0015c7902ade5cd477 Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Wed, 26 Jul 2023 10:45:14 -0700
Subject: [PATCH 35/41] fixed name in a parameter

---
 modules/skyline.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/skyline.nf b/modules/skyline.nf
index 4f75ba2..005ee0e 100644
--- a/modules/skyline.nf
+++ b/modules/skyline.nf
@@ -28,7 +28,7 @@ process SKYLINE_ADD_LIB {
         --tran-precursor-ion-charges="2, 3 ,4" \
         --tran-product-ion-charges="1,2" \
         --tran-product-ion-types="b, y, p" \
-        --tran-use-dia-exclusion \
+        --tran-use-dia-window-exclusion \
         --library-pick-product-ions="all_plus" \
         --tran-product-start-ion="ion 2" \
         --tran-product-end-ion="last ion - 2" \

From f70505b1c02f3edbccbd4b0cd2be8ef5aa8623a2 Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Wed, 26 Jul 2023 11:01:49 -0700
Subject: [PATCH 36/41] fixed name in a parameter

---
 modules/skyline.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/skyline.nf b/modules/skyline.nf
index 005ee0e..55daddd 100644
--- a/modules/skyline.nf
+++ b/modules/skyline.nf
@@ -161,7 +161,7 @@ process SKYLINE_MERGE_RESULTS {
         --reintegrate-model-name="reintegration_res" \
         --reintegrate-create-model \
         --full-scan-filter-tolerance=2 \
-        $\{import_extra_params} \
+        \${import_extra_params} \
         2>&1 | tee  "skyline-merge.log"
 
     echo "Directory status >>>>"

From 698b31d993d01d99bd58a5f62b5f5afa5231f876 Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Wed, 26 Jul 2023 11:17:21 -0700
Subject: [PATCH 37/41] fixed name in a parameter

---
 modules/skyline.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/skyline.nf b/modules/skyline.nf
index 55daddd..159279f 100644
--- a/modules/skyline.nf
+++ b/modules/skyline.nf
@@ -32,7 +32,8 @@ process SKYLINE_ADD_LIB {
         --library-pick-product-ions="all_plus" \
         --tran-product-start-ion="ion 2" \
         --tran-product-end-ion="last ion - 2" \
-        --associate-protein-group-proteins \
+        --associate-proteins-minimal-protein-list \
+        --associate-proteins-group-proteins \
         --full-scan-product-res=10.0 \
         --full-scan-product-analyzer=centroided \
         --full-scan-acquisition-method="DIA" \

From 091a088cb107b5404d04dc36b16b6b64c432cd39 Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Wed, 26 Jul 2023 12:30:52 -0700
Subject: [PATCH 38/41] moved parameters from termplate to import

---
 modules/skyline.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/skyline.nf b/modules/skyline.nf
index 159279f..506a939 100644
--- a/modules/skyline.nf
+++ b/modules/skyline.nf
@@ -36,7 +36,6 @@ process SKYLINE_ADD_LIB {
         --associate-proteins-group-proteins \
         --full-scan-product-res=10.0 \
         --full-scan-product-analyzer=centroided \
-        --full-scan-acquisition-method="DIA" \
         2>&1 | tee skyline_add_library.log \
     """
 
@@ -81,6 +80,7 @@ process SKYLINE_IMPORT_DATA {
         --in="${skyline_zipfile.baseName}" \
         --import-no-join \
         --import-file="\${local_rawfile}" \
+        --full-scan-acquisition-method="DIA" \
         \${import_extra_params} \
         2>&1 | tee  "${raw_file.baseName}.log"
     """

From d30a1d056e58dd3990cb8ad66e3ee27fd0c334f1 Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Wed, 26 Jul 2023 12:58:05 -0700
Subject: [PATCH 39/41] added rt filter

---
 modules/skyline.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/skyline.nf b/modules/skyline.nf
index 506a939..578666b 100644
--- a/modules/skyline.nf
+++ b/modules/skyline.nf
@@ -36,6 +36,7 @@ process SKYLINE_ADD_LIB {
         --associate-proteins-group-proteins \
         --full-scan-product-res=10.0 \
         --full-scan-product-analyzer=centroided \
+        --full-scan-rt-filter-tolerance=2 \
         2>&1 | tee skyline_add_library.log \
     """
 
@@ -161,7 +162,6 @@ process SKYLINE_MERGE_RESULTS {
         --share-type="complete" \
         --reintegrate-model-name="reintegration_res" \
         --reintegrate-create-model \
-        --full-scan-filter-tolerance=2 \
         \${import_extra_params} \
         2>&1 | tee  "skyline-merge.log"
 

From f433d2b44ed30675f93be7c8c76a685ccfc9f3a1 Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Fri, 28 Jul 2023 15:34:56 -0700
Subject: [PATCH 40/41] moved ims params to sky template creation

---
 modules/skyline.nf | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/modules/skyline.nf b/modules/skyline.nf
index 578666b..eb9e0f7 100644
--- a/modules/skyline.nf
+++ b/modules/skyline.nf
@@ -1,3 +1,6 @@
+
+// Code modified from 
+
 process SKYLINE_ADD_LIB {
     publishDir "${params.result_dir}/skyline/", failOnError: true, mode: 'copy'
     label 'process_medium'
@@ -37,6 +40,7 @@ process SKYLINE_ADD_LIB {
         --full-scan-product-res=10.0 \
         --full-scan-product-analyzer=centroided \
         --full-scan-rt-filter-tolerance=2 \
+        --ims-library-res=30 \
         2>&1 | tee skyline_add_library.log \
     """
 
@@ -71,7 +75,7 @@ process SKYLINE_IMPORT_DATA {
     if [[ ${raw_file} == *.d.tar ]] ; then
         tar -xvf ${raw_file}
         local_rawfile=\$(find \${PWD} -d -name "*.d")
-        import_extra_params=" --ims-library-res=30 --full-scan-isolation-scheme=\${local_rawfile}"
+        import_extra_params="  --full-scan-isolation-scheme=\${local_rawfile}"
     else
         local_rawfile=${raw_file}
         import_extra_params=" --full-scan-isolation-scheme=\${local_rawfile}"
@@ -136,7 +140,7 @@ process SKYLINE_MERGE_RESULTS {
     if [[ \$(find \${PWD} -type d -name "*.d") ]] ; then
         for f in *.d ; do
             import_files_params=" \${import_files_params} --import-file=\${f}"
-            import_extra_params=" --ims-library-res=30 --full-scan-isolation-scheme=\${f}"
+            import_extra_params=" --full-scan-isolation-scheme=\${f}"
         done
     fi
 

From ddae2d6417f08fc601c63ff1a0daa296eb7f877e Mon Sep 17 00:00:00 2001
From: "J. Sebastian Paez" <jspaezp@gmail.com>
Date: Fri, 28 Jul 2023 16:16:16 -0700
Subject: [PATCH 41/41] added mem logging and decoys

---
 modules/skyline.nf | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/modules/skyline.nf b/modules/skyline.nf
index eb9e0f7..3e76334 100644
--- a/modules/skyline.nf
+++ b/modules/skyline.nf
@@ -1,5 +1,5 @@
 
-// Code modified from 
+// Code modified from https://github.com/mriffle/nf-teirex-dia/blob/main/modules/skyline.nf
 
 process SKYLINE_ADD_LIB {
     publishDir "${params.result_dir}/skyline/", failOnError: true, mode: 'copy'
@@ -41,6 +41,9 @@ process SKYLINE_ADD_LIB {
         --full-scan-product-analyzer=centroided \
         --full-scan-rt-filter-tolerance=2 \
         --ims-library-res=30 \
+        --decoys-add=shuffle \
+        --timestamp \
+        --memstamp \
         2>&1 | tee skyline_add_library.log \
     """
 
@@ -86,6 +89,8 @@ process SKYLINE_IMPORT_DATA {
         --import-no-join \
         --import-file="\${local_rawfile}" \
         --full-scan-acquisition-method="DIA" \
+        --timestamp \
+        --memstamp \
         \${import_extra_params} \
         2>&1 | tee  "${raw_file.baseName}.log"
     """
@@ -166,6 +171,8 @@ process SKYLINE_MERGE_RESULTS {
         --share-type="complete" \
         --reintegrate-model-name="reintegration_res" \
         --reintegrate-create-model \
+        --timestamp \
+        --memstamp \
         \${import_extra_params} \
         2>&1 | tee  "skyline-merge.log"