Longqc 1.2.3

[RaheelSyedAhmed]

Pull Request (PR) checklist:

• Include a description of what is in this pull request in this message.
• The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/build-files/samtools/1.15 )
• Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number in build-files (i.e. docker-builds/build-files/spades/3.12.0/Dockerfile)
  • (optional) All test files are located in same directory as the Dockerfile (i.e. build-files/shigatyper/2.0.1/test.sh)
• Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. docker-builds/build-files/spades/3.12.0/README.md)
  • If this README is longer than 30 lines, there is an explanation as to why more detail was needed
• Dockerfile includes the recommended LABELS
• Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
• Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

Addition of LongQC tool version 1.2.3. Main README.md should be updated to have base information and version 1.2.3 in the versions dropdown. An MIT license is linked in the Program Licenses file. The program README.md has information as specified by the template and it's larger than 30 lines because the author included some extra examples to indicate preset / preparation kit selection.

I would like to keep this as a draft PR for now. I'm thinking of any way I can optimize the build stage, and if it's acceptable to copy over python site-packages from a builder stage.

[RaheelSyedAhmed]

Decided on usage builder stage for main Dockerfile; we use venv for proper copying from the builder stage to the app stage, and avoid installing those extra development libraries with apt-get.

[Kincekara]

Could you add a test using a PacBio BAM file? A demultiplexed HiFi read is available here:
https://downloads.pacbcloud.com/public/dataset/2021-11-Microbial-96plex/demultiplexed-reads/
There are plenty of ONT examples available, but not many for PacBio, and the tool has been a bit buggy. Having this test in place would help ensure everything works correctly.

[RaheelSyedAhmed]

Could you add a test using a PacBio BAM file? A demultiplexed HiFi read is available here: https://downloads.pacbcloud.com/public/dataset/2021-11-Microbial-96plex/demultiplexed-reads/ There are plenty of ONT examples available, but not many for PacBio, and the tool has been a bit buggy. Having this test in place would help ensure everything works correctly.

I added a PacBio test from the url you supplied. Unfortunately, I did run into issues 14 and 76 from longQC's issues page with some of the BAM files I tested. However, the test case I have added in a2333c9 has successfully ran, and I'll supply the stats from the output JSON below for your review.

JSON output:

{
    "Yield": 153957194,
    "Q7 bases": "0.00%",
    "Longest_read": 19781,
    "Num_of_reads": 24874,
    "Length_stats": {
        "gamma_params": [
            3.914445661304276,
            1581.190106752738
        ],
        "Mean_read_length": 6189.4827530755,
        "N50_read_length": 7501.0
    },
    "GC_stats": {
        "Mean_GC_content": 0.35441556572914124,
        "SD_GC_content": 0.027690311893820763
    },
    "Stats_for_adapter5": {
        "Num_of_trimmed_reads_5": 1,
        "Max_identity_adp5": 0.782608695652174,
        "Average_position_from_5_end": 46.0
    },
    "Coverage_stats": {
        "Estimated non-sense read fraction": 0.00020165355918531962,
        "Mean_coverage": 26.705123957226252,
        "SD_coverage": 2.513672150253549,
        "Estimated crude Xome size": "5763918 (e = 0.0%)"
    }
} 

[erinyoung]

Closes #1650