From e3db36c11f7a48050a54bea9b5831726d7ebc6b5 Mon Sep 17 00:00:00 2001 From: Kevin-Brockers Date: Sat, 20 Jun 2026 08:36:57 +0200 Subject: [PATCH 1/5] changed the bedgraph suffix from .mLB. to .mLb. --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index dd167875..9022081e 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -449,7 +449,7 @@ process { args << "-bga" return args.join(' ') } - ext.prefix = { "${meta.id}.mLB.clN" } + ext.prefix = { "${meta.id}.mLb.clN" } publishDir = [ [ path: { "${params.outdir}/${params.aligner}/merged_library/bigwig" }, From 9f13397e8328cba0e9be001ea5287bde9d2941c2 Mon Sep 17 00:00:00 2001 From: Kevin-Brockers Date: Sat, 20 Jun 2026 09:59:59 +0200 Subject: [PATCH 2/5] Updated snapshots --- tests/bowtie2.nf.test.snap | 30 ++++++++++++------------- tests/chromap.nf.test.snap | 30 ++++++++++++------------- tests/default.nf.test.snap | 30 ++++++++++++------------- tests/skip_consensus_peaks.nf.test.snap | 30 ++++++++++++------------- tests/skip_trimming.nf.test.snap | 30 ++++++++++++------------- tests/star.nf.test.snap | 30 ++++++++++++------------- 6 files changed, 90 insertions(+), 90 deletions(-) diff --git a/tests/bowtie2.nf.test.snap b/tests/bowtie2.nf.test.snap index b201e978..dc0e003f 100644 --- a/tests/bowtie2.nf.test.snap +++ b/tests/bowtie2.nf.test.snap @@ -134,17 +134,17 @@ "bowtie2/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam", "bowtie2/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam.bai", "bowtie2/merged_library/bigwig", - "bowtie2/merged_library/bigwig/SPT5_INPUT_REP1.mLB.clN.bedGraph", + "bowtie2/merged_library/bigwig/SPT5_INPUT_REP1.mLb.clN.bedGraph", "bowtie2/merged_library/bigwig/SPT5_INPUT_REP1.mLb.clN.bigWig", - "bowtie2/merged_library/bigwig/SPT5_INPUT_REP2.mLB.clN.bedGraph", + "bowtie2/merged_library/bigwig/SPT5_INPUT_REP2.mLb.clN.bedGraph", "bowtie2/merged_library/bigwig/SPT5_INPUT_REP2.mLb.clN.bigWig", - "bowtie2/merged_library/bigwig/SPT5_T0_REP1.mLB.clN.bedGraph", + "bowtie2/merged_library/bigwig/SPT5_T0_REP1.mLb.clN.bedGraph", "bowtie2/merged_library/bigwig/SPT5_T0_REP1.mLb.clN.bigWig", - "bowtie2/merged_library/bigwig/SPT5_T0_REP2.mLB.clN.bedGraph", + "bowtie2/merged_library/bigwig/SPT5_T0_REP2.mLb.clN.bedGraph", "bowtie2/merged_library/bigwig/SPT5_T0_REP2.mLb.clN.bigWig", - "bowtie2/merged_library/bigwig/SPT5_T15_REP1.mLB.clN.bedGraph", + "bowtie2/merged_library/bigwig/SPT5_T15_REP1.mLb.clN.bedGraph", "bowtie2/merged_library/bigwig/SPT5_T15_REP1.mLb.clN.bigWig", - "bowtie2/merged_library/bigwig/SPT5_T15_REP2.mLB.clN.bedGraph", + "bowtie2/merged_library/bigwig/SPT5_T15_REP2.mLb.clN.bedGraph", "bowtie2/merged_library/bigwig/SPT5_T15_REP2.mLb.clN.bigWig", "bowtie2/merged_library/deepTools", "bowtie2/merged_library/deepTools/plotFingerprint", @@ -808,12 +808,12 @@ "trimgalore/logs/SPT5_T15_REP2_T1_2.fastq.gz_trimming_report.txt" ], [ - "SPT5_INPUT_REP1.mLB.clN.bedGraph:md5,3185527dd339a8dbcca453f97ecc0860", - "SPT5_INPUT_REP2.mLB.clN.bedGraph:md5,bdc6ce913840caa034fe12f11dc3f821", - "SPT5_T0_REP1.mLB.clN.bedGraph:md5,a1c995094ac610f67f74037882713be1", - "SPT5_T0_REP2.mLB.clN.bedGraph:md5,ac8049a66f664f4f52e55738bb1b8482", - "SPT5_T15_REP1.mLB.clN.bedGraph:md5,6594e02d144dcf85f39b5c7339e11db6", - "SPT5_T15_REP2.mLB.clN.bedGraph:md5,3afb695bb7014e0d8df83cda30d4731d", + "SPT5_INPUT_REP1.mLb.clN.bedGraph:md5,3185527dd339a8dbcca453f97ecc0860", + "SPT5_INPUT_REP2.mLb.clN.bedGraph:md5,bdc6ce913840caa034fe12f11dc3f821", + "SPT5_T0_REP1.mLb.clN.bedGraph:md5,a1c995094ac610f67f74037882713be1", + "SPT5_T0_REP2.mLb.clN.bedGraph:md5,ac8049a66f664f4f52e55738bb1b8482", + "SPT5_T15_REP1.mLb.clN.bedGraph:md5,6594e02d144dcf85f39b5c7339e11db6", + "SPT5_T15_REP2.mLb.clN.bedGraph:md5,3afb695bb7014e0d8df83cda30d4731d", "SPT5_T0_REP1_peaks.broadPeak:md5,27d134afd2953dafa22e35dcf8ec2bcc", "SPT5_T0_REP1_peaks.gappedPeak:md5,f221f53d1a6486714ad50664ef440ca7", "SPT5_T0_REP1_peaks.xls:md5,5cd75fde29ae6f23e7eeebd9da4bcfd9", @@ -946,10 +946,10 @@ "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" ] ], - "timestamp": "2026-03-26T13:38:56.98274", + "timestamp": "2026-06-20T09:06:05.68183", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.04.0" + "nf-test": "0.9.5", + "nextflow": "26.04.0" } }, "bowtie2 with stub": { diff --git a/tests/chromap.nf.test.snap b/tests/chromap.nf.test.snap index cb1b94ff..d4eed2de 100644 --- a/tests/chromap.nf.test.snap +++ b/tests/chromap.nf.test.snap @@ -126,17 +126,17 @@ "chromap/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam", "chromap/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam.bai", "chromap/merged_library/bigwig", - "chromap/merged_library/bigwig/SPT5_INPUT_REP1.mLB.clN.bedGraph", + "chromap/merged_library/bigwig/SPT5_INPUT_REP1.mLb.clN.bedGraph", "chromap/merged_library/bigwig/SPT5_INPUT_REP1.mLb.clN.bigWig", - "chromap/merged_library/bigwig/SPT5_INPUT_REP2.mLB.clN.bedGraph", + "chromap/merged_library/bigwig/SPT5_INPUT_REP2.mLb.clN.bedGraph", "chromap/merged_library/bigwig/SPT5_INPUT_REP2.mLb.clN.bigWig", - "chromap/merged_library/bigwig/SPT5_T0_REP1.mLB.clN.bedGraph", + "chromap/merged_library/bigwig/SPT5_T0_REP1.mLb.clN.bedGraph", "chromap/merged_library/bigwig/SPT5_T0_REP1.mLb.clN.bigWig", - "chromap/merged_library/bigwig/SPT5_T0_REP2.mLB.clN.bedGraph", + "chromap/merged_library/bigwig/SPT5_T0_REP2.mLb.clN.bedGraph", "chromap/merged_library/bigwig/SPT5_T0_REP2.mLb.clN.bigWig", - "chromap/merged_library/bigwig/SPT5_T15_REP1.mLB.clN.bedGraph", + "chromap/merged_library/bigwig/SPT5_T15_REP1.mLb.clN.bedGraph", "chromap/merged_library/bigwig/SPT5_T15_REP1.mLb.clN.bigWig", - "chromap/merged_library/bigwig/SPT5_T15_REP2.mLB.clN.bedGraph", + "chromap/merged_library/bigwig/SPT5_T15_REP2.mLb.clN.bedGraph", "chromap/merged_library/bigwig/SPT5_T15_REP2.mLb.clN.bigWig", "chromap/merged_library/deepTools", "chromap/merged_library/deepTools/plotFingerprint", @@ -803,12 +803,12 @@ "trimgalore/logs/SPT5_T15_REP2_T1_2.fastq.gz_trimming_report.txt" ], [ - "SPT5_INPUT_REP1.mLB.clN.bedGraph:md5,e18a171dc9e71782335f2ca933da0773", - "SPT5_INPUT_REP2.mLB.clN.bedGraph:md5,3155c2b26db574cfccbb0388dea6617a", - "SPT5_T0_REP1.mLB.clN.bedGraph:md5,2497e5d9197400d42d51641f82c017b3", - "SPT5_T0_REP2.mLB.clN.bedGraph:md5,552f2dc1010cea4e1d822081409bb11b", - "SPT5_T15_REP1.mLB.clN.bedGraph:md5,52c8de5177ed6d20c2e598d9d9717de4", - "SPT5_T15_REP2.mLB.clN.bedGraph:md5,66db76ce702dea56dd5fb9a8b261a7fb", + "SPT5_INPUT_REP1.mLb.clN.bedGraph:md5,e18a171dc9e71782335f2ca933da0773", + "SPT5_INPUT_REP2.mLb.clN.bedGraph:md5,3155c2b26db574cfccbb0388dea6617a", + "SPT5_T0_REP1.mLb.clN.bedGraph:md5,2497e5d9197400d42d51641f82c017b3", + "SPT5_T0_REP2.mLb.clN.bedGraph:md5,552f2dc1010cea4e1d822081409bb11b", + "SPT5_T15_REP1.mLb.clN.bedGraph:md5,52c8de5177ed6d20c2e598d9d9717de4", + "SPT5_T15_REP2.mLb.clN.bedGraph:md5,66db76ce702dea56dd5fb9a8b261a7fb", "SPT5_T0_REP1_peaks.broadPeak:md5,b4a7e2305ed63853b04d5e18678ea27a", "SPT5_T0_REP1_peaks.gappedPeak:md5,2765b191811a573296f0122b9a270e4b", "SPT5_T0_REP1_peaks.xls:md5,c98206fe98326026daf9f76a72de3e5b", @@ -942,10 +942,10 @@ "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" ] ], - "timestamp": "2026-03-26T13:48:17.847211", + "timestamp": "2026-06-20T09:16:06.518313", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.04.0" + "nf-test": "0.9.5", + "nextflow": "26.04.0" } }, "chromap with stub": { diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index b65c99a2..d14cf61b 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -133,17 +133,17 @@ "bwa/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam", "bwa/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam.bai", "bwa/merged_library/bigwig", - "bwa/merged_library/bigwig/SPT5_INPUT_REP1.mLB.clN.bedGraph", + "bwa/merged_library/bigwig/SPT5_INPUT_REP1.mLb.clN.bedGraph", "bwa/merged_library/bigwig/SPT5_INPUT_REP1.mLb.clN.bigWig", - "bwa/merged_library/bigwig/SPT5_INPUT_REP2.mLB.clN.bedGraph", + "bwa/merged_library/bigwig/SPT5_INPUT_REP2.mLb.clN.bedGraph", "bwa/merged_library/bigwig/SPT5_INPUT_REP2.mLb.clN.bigWig", - "bwa/merged_library/bigwig/SPT5_T0_REP1.mLB.clN.bedGraph", + "bwa/merged_library/bigwig/SPT5_T0_REP1.mLb.clN.bedGraph", "bwa/merged_library/bigwig/SPT5_T0_REP1.mLb.clN.bigWig", - "bwa/merged_library/bigwig/SPT5_T0_REP2.mLB.clN.bedGraph", + "bwa/merged_library/bigwig/SPT5_T0_REP2.mLb.clN.bedGraph", "bwa/merged_library/bigwig/SPT5_T0_REP2.mLb.clN.bigWig", - "bwa/merged_library/bigwig/SPT5_T15_REP1.mLB.clN.bedGraph", + "bwa/merged_library/bigwig/SPT5_T15_REP1.mLb.clN.bedGraph", "bwa/merged_library/bigwig/SPT5_T15_REP1.mLb.clN.bigWig", - "bwa/merged_library/bigwig/SPT5_T15_REP2.mLB.clN.bedGraph", + "bwa/merged_library/bigwig/SPT5_T15_REP2.mLb.clN.bedGraph", "bwa/merged_library/bigwig/SPT5_T15_REP2.mLb.clN.bigWig", "bwa/merged_library/deepTools", "bwa/merged_library/deepTools/plotFingerprint", @@ -807,12 +807,12 @@ "trimgalore/logs/SPT5_T15_REP2_T1_2.fastq.gz_trimming_report.txt" ], [ - "SPT5_INPUT_REP1.mLB.clN.bedGraph:md5,0a93a9e9e1c5c89f62050e0a2c12ca31", - "SPT5_INPUT_REP2.mLB.clN.bedGraph:md5,729d6cd9bd4e7a1e8ffc2f1cadc6483e", - "SPT5_T0_REP1.mLB.clN.bedGraph:md5,7d6d55a647a218f65b2b1653ba4b930d", - "SPT5_T0_REP2.mLB.clN.bedGraph:md5,b6d1bb76e3dcb321d010762ca8046fa6", - "SPT5_T15_REP1.mLB.clN.bedGraph:md5,2e0f7340ba33729e7a46f75965168481", - "SPT5_T15_REP2.mLB.clN.bedGraph:md5,a013dd85f9fdbd134b51058260bf7941", + "SPT5_INPUT_REP1.mLb.clN.bedGraph:md5,0a93a9e9e1c5c89f62050e0a2c12ca31", + "SPT5_INPUT_REP2.mLb.clN.bedGraph:md5,729d6cd9bd4e7a1e8ffc2f1cadc6483e", + "SPT5_T0_REP1.mLb.clN.bedGraph:md5,7d6d55a647a218f65b2b1653ba4b930d", + "SPT5_T0_REP2.mLb.clN.bedGraph:md5,b6d1bb76e3dcb321d010762ca8046fa6", + "SPT5_T15_REP1.mLb.clN.bedGraph:md5,2e0f7340ba33729e7a46f75965168481", + "SPT5_T15_REP2.mLb.clN.bedGraph:md5,a013dd85f9fdbd134b51058260bf7941", "SPT5_T0_REP1_peaks.broadPeak:md5,0574cd91ce590e3be41c9057c6d4ea25", "SPT5_T0_REP1_peaks.gappedPeak:md5,95203ab9aa297a4c52a4c8bbc8603fd7", "SPT5_T0_REP1_peaks.xls:md5,f2dc646828f6d1da711e8c57f939b1fa", @@ -945,10 +945,10 @@ "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" ] ], - "timestamp": "2026-03-26T13:57:56.16437", + "timestamp": "2026-06-20T09:26:27.903591", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.04.0" + "nf-test": "0.9.5", + "nextflow": "26.04.0" } } } \ No newline at end of file diff --git a/tests/skip_consensus_peaks.nf.test.snap b/tests/skip_consensus_peaks.nf.test.snap index 977ee3f4..5407db11 100644 --- a/tests/skip_consensus_peaks.nf.test.snap +++ b/tests/skip_consensus_peaks.nf.test.snap @@ -129,17 +129,17 @@ "bwa/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam", "bwa/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam.bai", "bwa/merged_library/bigwig", - "bwa/merged_library/bigwig/SPT5_INPUT_REP1.mLB.clN.bedGraph", + "bwa/merged_library/bigwig/SPT5_INPUT_REP1.mLb.clN.bedGraph", "bwa/merged_library/bigwig/SPT5_INPUT_REP1.mLb.clN.bigWig", - "bwa/merged_library/bigwig/SPT5_INPUT_REP2.mLB.clN.bedGraph", + "bwa/merged_library/bigwig/SPT5_INPUT_REP2.mLb.clN.bedGraph", "bwa/merged_library/bigwig/SPT5_INPUT_REP2.mLb.clN.bigWig", - "bwa/merged_library/bigwig/SPT5_T0_REP1.mLB.clN.bedGraph", + "bwa/merged_library/bigwig/SPT5_T0_REP1.mLb.clN.bedGraph", "bwa/merged_library/bigwig/SPT5_T0_REP1.mLb.clN.bigWig", - "bwa/merged_library/bigwig/SPT5_T0_REP2.mLB.clN.bedGraph", + "bwa/merged_library/bigwig/SPT5_T0_REP2.mLb.clN.bedGraph", "bwa/merged_library/bigwig/SPT5_T0_REP2.mLb.clN.bigWig", - "bwa/merged_library/bigwig/SPT5_T15_REP1.mLB.clN.bedGraph", + "bwa/merged_library/bigwig/SPT5_T15_REP1.mLb.clN.bedGraph", "bwa/merged_library/bigwig/SPT5_T15_REP1.mLb.clN.bigWig", - "bwa/merged_library/bigwig/SPT5_T15_REP2.mLB.clN.bedGraph", + "bwa/merged_library/bigwig/SPT5_T15_REP2.mLb.clN.bedGraph", "bwa/merged_library/bigwig/SPT5_T15_REP2.mLb.clN.bigWig", "bwa/merged_library/deepTools", "bwa/merged_library/deepTools/plotFingerprint", @@ -760,12 +760,12 @@ "trimgalore/logs/SPT5_T15_REP2_T1_2.fastq.gz_trimming_report.txt" ], [ - "SPT5_INPUT_REP1.mLB.clN.bedGraph:md5,0a93a9e9e1c5c89f62050e0a2c12ca31", - "SPT5_INPUT_REP2.mLB.clN.bedGraph:md5,729d6cd9bd4e7a1e8ffc2f1cadc6483e", - "SPT5_T0_REP1.mLB.clN.bedGraph:md5,7d6d55a647a218f65b2b1653ba4b930d", - "SPT5_T0_REP2.mLB.clN.bedGraph:md5,b6d1bb76e3dcb321d010762ca8046fa6", - "SPT5_T15_REP1.mLB.clN.bedGraph:md5,2e0f7340ba33729e7a46f75965168481", - "SPT5_T15_REP2.mLB.clN.bedGraph:md5,a013dd85f9fdbd134b51058260bf7941", + "SPT5_INPUT_REP1.mLb.clN.bedGraph:md5,0a93a9e9e1c5c89f62050e0a2c12ca31", + "SPT5_INPUT_REP2.mLb.clN.bedGraph:md5,729d6cd9bd4e7a1e8ffc2f1cadc6483e", + "SPT5_T0_REP1.mLb.clN.bedGraph:md5,7d6d55a647a218f65b2b1653ba4b930d", + "SPT5_T0_REP2.mLb.clN.bedGraph:md5,b6d1bb76e3dcb321d010762ca8046fa6", + "SPT5_T15_REP1.mLb.clN.bedGraph:md5,2e0f7340ba33729e7a46f75965168481", + "SPT5_T15_REP2.mLb.clN.bedGraph:md5,a013dd85f9fdbd134b51058260bf7941", "SPT5_T0_REP1_peaks.broadPeak:md5,0574cd91ce590e3be41c9057c6d4ea25", "SPT5_T0_REP1_peaks.gappedPeak:md5,95203ab9aa297a4c52a4c8bbc8603fd7", "SPT5_T0_REP1_peaks.xls:md5,f2dc646828f6d1da711e8c57f939b1fa", @@ -886,10 +886,10 @@ "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" ] ], - "timestamp": "2026-03-26T14:06:46.726058", + "timestamp": "2026-06-20T09:35:30.906145", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.04.0" + "nf-test": "0.9.5", + "nextflow": "26.04.0" } } } \ No newline at end of file diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index 78b20cd5..4405a0c8 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -130,17 +130,17 @@ "bwa/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam", "bwa/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam.bai", "bwa/merged_library/bigwig", - "bwa/merged_library/bigwig/SPT5_INPUT_REP1.mLB.clN.bedGraph", + "bwa/merged_library/bigwig/SPT5_INPUT_REP1.mLb.clN.bedGraph", "bwa/merged_library/bigwig/SPT5_INPUT_REP1.mLb.clN.bigWig", - "bwa/merged_library/bigwig/SPT5_INPUT_REP2.mLB.clN.bedGraph", + "bwa/merged_library/bigwig/SPT5_INPUT_REP2.mLb.clN.bedGraph", "bwa/merged_library/bigwig/SPT5_INPUT_REP2.mLb.clN.bigWig", - "bwa/merged_library/bigwig/SPT5_T0_REP1.mLB.clN.bedGraph", + "bwa/merged_library/bigwig/SPT5_T0_REP1.mLb.clN.bedGraph", "bwa/merged_library/bigwig/SPT5_T0_REP1.mLb.clN.bigWig", - "bwa/merged_library/bigwig/SPT5_T0_REP2.mLB.clN.bedGraph", + "bwa/merged_library/bigwig/SPT5_T0_REP2.mLb.clN.bedGraph", "bwa/merged_library/bigwig/SPT5_T0_REP2.mLb.clN.bigWig", - "bwa/merged_library/bigwig/SPT5_T15_REP1.mLB.clN.bedGraph", + "bwa/merged_library/bigwig/SPT5_T15_REP1.mLb.clN.bedGraph", "bwa/merged_library/bigwig/SPT5_T15_REP1.mLb.clN.bigWig", - "bwa/merged_library/bigwig/SPT5_T15_REP2.mLB.clN.bedGraph", + "bwa/merged_library/bigwig/SPT5_T15_REP2.mLb.clN.bedGraph", "bwa/merged_library/bigwig/SPT5_T15_REP2.mLb.clN.bigWig", "bwa/merged_library/deepTools", "bwa/merged_library/deepTools/plotFingerprint", @@ -700,12 +700,12 @@ "pipeline_info/samplesheet.valid.csv" ], [ - "SPT5_INPUT_REP1.mLB.clN.bedGraph:md5,cd382620d1d0b392cc476acb3ee5b64c", - "SPT5_INPUT_REP2.mLB.clN.bedGraph:md5,adeb44bad86ea7074ac4900b8d04e1e9", - "SPT5_T0_REP1.mLB.clN.bedGraph:md5,9169ca9f49eb70a6d282b00d94e8bbb0", - "SPT5_T0_REP2.mLB.clN.bedGraph:md5,0155d0171022e7cef596facf4d4f12f7", - "SPT5_T15_REP1.mLB.clN.bedGraph:md5,53acbef45032a4c58766c9d220e1a761", - "SPT5_T15_REP2.mLB.clN.bedGraph:md5,d2fbf8ad95d452e738f36081d51e4d22", + "SPT5_INPUT_REP1.mLb.clN.bedGraph:md5,cd382620d1d0b392cc476acb3ee5b64c", + "SPT5_INPUT_REP2.mLb.clN.bedGraph:md5,adeb44bad86ea7074ac4900b8d04e1e9", + "SPT5_T0_REP1.mLb.clN.bedGraph:md5,9169ca9f49eb70a6d282b00d94e8bbb0", + "SPT5_T0_REP2.mLb.clN.bedGraph:md5,0155d0171022e7cef596facf4d4f12f7", + "SPT5_T15_REP1.mLb.clN.bedGraph:md5,53acbef45032a4c58766c9d220e1a761", + "SPT5_T15_REP2.mLb.clN.bedGraph:md5,d2fbf8ad95d452e738f36081d51e4d22", "SPT5_T0_REP1_peaks.broadPeak:md5,ddf2e346dd0b80bd433c09312d31cb51", "SPT5_T0_REP1_peaks.gappedPeak:md5,38996ca713aeb8069165e347e69bed89", "SPT5_T0_REP1_peaks.xls:md5,d68f4b095c466fccb5c65c8807f142a2", @@ -823,10 +823,10 @@ "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" ] ], - "timestamp": "2026-03-26T14:16:04.604869", + "timestamp": "2026-06-20T09:44:50.992423", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.04.0" + "nf-test": "0.9.5", + "nextflow": "26.04.0" } }, "skip_trimming with stub": { diff --git a/tests/star.nf.test.snap b/tests/star.nf.test.snap index a139cab1..2003110e 100644 --- a/tests/star.nf.test.snap +++ b/tests/star.nf.test.snap @@ -551,17 +551,17 @@ "star/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam", "star/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam.bai", "star/merged_library/bigwig", - "star/merged_library/bigwig/SPT5_INPUT_REP1.mLB.clN.bedGraph", + "star/merged_library/bigwig/SPT5_INPUT_REP1.mLb.clN.bedGraph", "star/merged_library/bigwig/SPT5_INPUT_REP1.mLb.clN.bigWig", - "star/merged_library/bigwig/SPT5_INPUT_REP2.mLB.clN.bedGraph", + "star/merged_library/bigwig/SPT5_INPUT_REP2.mLb.clN.bedGraph", "star/merged_library/bigwig/SPT5_INPUT_REP2.mLb.clN.bigWig", - "star/merged_library/bigwig/SPT5_T0_REP1.mLB.clN.bedGraph", + "star/merged_library/bigwig/SPT5_T0_REP1.mLb.clN.bedGraph", "star/merged_library/bigwig/SPT5_T0_REP1.mLb.clN.bigWig", - "star/merged_library/bigwig/SPT5_T0_REP2.mLB.clN.bedGraph", + "star/merged_library/bigwig/SPT5_T0_REP2.mLb.clN.bedGraph", "star/merged_library/bigwig/SPT5_T0_REP2.mLb.clN.bigWig", - "star/merged_library/bigwig/SPT5_T15_REP1.mLB.clN.bedGraph", + "star/merged_library/bigwig/SPT5_T15_REP1.mLb.clN.bedGraph", "star/merged_library/bigwig/SPT5_T15_REP1.mLb.clN.bigWig", - "star/merged_library/bigwig/SPT5_T15_REP2.mLB.clN.bedGraph", + "star/merged_library/bigwig/SPT5_T15_REP2.mLb.clN.bedGraph", "star/merged_library/bigwig/SPT5_T15_REP2.mLb.clN.bigWig", "star/merged_library/deepTools", "star/merged_library/deepTools/plotFingerprint", @@ -927,12 +927,12 @@ "SPT5_T0_REP2_T1.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", "SPT5_T15_REP1_T1.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", "SPT5_T15_REP2_T1.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "SPT5_INPUT_REP1.mLB.clN.bedGraph:md5,27ec9b3ea78e51a6747f10e87fb28e75", - "SPT5_INPUT_REP2.mLB.clN.bedGraph:md5,0f5eaf0b37296d9a39240163d428d3da", - "SPT5_T0_REP1.mLB.clN.bedGraph:md5,16be7d838c6ccb52a7205d6affe4856a", - "SPT5_T0_REP2.mLB.clN.bedGraph:md5,7fe898c6cdf6d00ff90144ba391bb9df", - "SPT5_T15_REP1.mLB.clN.bedGraph:md5,2ab1546e5cf69c46f0340054a8f78efd", - "SPT5_T15_REP2.mLB.clN.bedGraph:md5,04a755253939b714f9fe92667ceecad2", + "SPT5_INPUT_REP1.mLb.clN.bedGraph:md5,27ec9b3ea78e51a6747f10e87fb28e75", + "SPT5_INPUT_REP2.mLb.clN.bedGraph:md5,0f5eaf0b37296d9a39240163d428d3da", + "SPT5_T0_REP1.mLb.clN.bedGraph:md5,16be7d838c6ccb52a7205d6affe4856a", + "SPT5_T0_REP2.mLb.clN.bedGraph:md5,7fe898c6cdf6d00ff90144ba391bb9df", + "SPT5_T15_REP1.mLb.clN.bedGraph:md5,2ab1546e5cf69c46f0340054a8f78efd", + "SPT5_T15_REP2.mLb.clN.bedGraph:md5,04a755253939b714f9fe92667ceecad2", "SPT5_T0_REP1_peaks.broadPeak:md5,5c48f4161896e2e5b19524737643ad95", "SPT5_T0_REP1_peaks.gappedPeak:md5,15e0b902c54e444514e555a096468ed6", "SPT5_T0_REP1_peaks.xls:md5,713e133e92dc3f9829be9f560667b399", @@ -977,10 +977,10 @@ "SPT5_T15_REP2.mLb.clN.sorted.bam.idxstats:md5,aa2db2bcb3aa876cfbfe24b49d98aabd" ] ], - "timestamp": "2026-03-26T14:28:39.102565", + "timestamp": "2026-06-20T09:59:04.660863", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.04.0" + "nf-test": "0.9.5", + "nextflow": "26.04.0" } }, "star with stub": { From 844bcacf73df5ea13066355be4c34be0a1e4f9f5 Mon Sep 17 00:00:00 2001 From: Kevin-Brockers Date: Sat, 20 Jun 2026 10:07:01 +0200 Subject: [PATCH 3/5] Updated Changelog --- CHANGELOG.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f8c7d85c..8ff0ccac 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -27,7 +27,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[#479](https://github.com/nf-core/chipseq/issues/479)] - Changed the usage documentation for antibodies to be required for IP samples. Since a ChIP IP sample will always have an antibody, it should be specified to distinguish the sample from input/controls. -- [[PR #514](https://github.com/nf-core/chipseq/pull/514)] - Updated pipeline template to [nf-core/tools 4.0.2](https://github.com/nf-core/tools/releases/tag/4.0.2) +- [[PR #514](https://github.com/nf-core/chipseq/pull/514)] - Updated pipeline template to [nf-core/tools + 4.0.2](https://github.com/nf-core/tools/releases/tag/4.0.2) +- [[PR #520] (https://github.com/nf-core/chipseq/pull/520)] - Changed merged librarie suffix to `.mLb.` ### Parameters From cdff59bea27974fc6ac36004698a9bb4c683e2c0 Mon Sep 17 00:00:00 2001 From: Jose Espinosa-Carrasco Date: Mon, 22 Jun 2026 12:24:44 +0200 Subject: [PATCH 4/5] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8ff0ccac..ab7e9f3e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -29,7 +29,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 the sample from input/controls. - [[PR #514](https://github.com/nf-core/chipseq/pull/514)] - Updated pipeline template to [nf-core/tools 4.0.2](https://github.com/nf-core/tools/releases/tag/4.0.2) -- [[PR #520] (https://github.com/nf-core/chipseq/pull/520)] - Changed merged librarie suffix to `.mLb.` +- [[#519] (https://github.com/nf-core/chipseq/issues/519)] - Changed merged libraries suffix to `.mLb.` ### Parameters From 7f3fb6c97e06017d41238f6fc7fae2fa8a096c37 Mon Sep 17 00:00:00 2001 From: Jose Espinosa-Carrasco Date: Mon, 22 Jun 2026 14:22:48 +0200 Subject: [PATCH 5/5] Apply suggestion from @JoseEspinosa --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ab7e9f3e..482859ca 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -28,8 +28,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 required for IP samples. Since a ChIP IP sample will always have an antibody, it should be specified to distinguish the sample from input/controls. - [[PR #514](https://github.com/nf-core/chipseq/pull/514)] - Updated pipeline template to [nf-core/tools - 4.0.2](https://github.com/nf-core/tools/releases/tag/4.0.2) -- [[#519] (https://github.com/nf-core/chipseq/issues/519)] - Changed merged libraries suffix to `.mLb.` + 4.0.2](https://github.com/nf-core/tools/releases/tag/4.0.2). +- [[#519] (https://github.com/nf-core/chipseq/issues/519)] - Changed merged libraries suffix to `.mLb.`. ### Parameters