Module/bclconvert (#1485)

* bclconvert: initial commit

* add most of tool

* attempt at adding testing stub

* add dockerfile + instructions

* add container to module

* update readme

* more attempts at making stubs work

* finish stub run

* fix ci issues

* more fixes to stub

* add read version check to stub

* fix some tests

* update readme

* fix version number

* syntax fix

* revert edit to output directory

* Update modules/bclconvert/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/bclconvert/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* update meta.yaml

* update thread usage

* Update modules/bclconvert/main.nf

Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>

* Escape env variable

* Update modules/bclconvert/Dockerfile

Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>

* fix comments by @Emiller88

* fix task.cpus

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>

modules/bclconvert/.gitignore

@@ -0,0 +1,2 @@
+bcl-convert
+*.rpm

modules/bclconvert/Dockerfile

@@ -0,0 +1,15 @@
+# Dockerfile to create container with bcl-convert
+# Push to nfcore/bclconvert:<VER>
+
+FROM debian:bullseye-slim
+LABEL authors="Matthias De Smet <matthias.desmet@ugent.be>" \
+    description="Docker image containing bcl-convert"
+# Disclaimer: this container is not provided nor supported by Illumina
+# 'ps' command is need by some nextflow executions to collect system stats
+# Install procps and clean apt cache
+RUN apt-get update \
+    && apt-get install -y \
+    procps \
+    && apt-get clean -y && rm -rf /var/lib/apt/lists/*
+COPY bcl-convert /usr/local/bin/bcl-convert
+RUN chmod +x /usr/local/bin/bcl-convert

modules/bclconvert/LICENSE

@@ -0,0 +1,30 @@
+ILLUMINA END-USER SOFTWARE LICENSE AGREEMENT
+
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+
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+END OF END-USER SOFTWARE LICENSE AGREEMENT.

modules/bclconvert/README.md

@@ -0,0 +1,17 @@
+# Updating the docker container and making a new module release
+
+bcl-convert is a commercial tool from Illumina. The container provided for the bcl-convert nf-core module is not provided nor supported by Illumina. Updating the bcl-convert versions in the container and pushing the update to Dockerhub needs to be done manually.
+
+1. Navigate to the appropriate download page. - [BCL Convert](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/downloads.html): download the rpm of the desired bcl-convert version with `curl` or `wget`.
+2. Unpack the RPM package using `rpm2cpio bcl-convert-*.rpm | cpio -i --make-directories`. Place the executable located in `<unpack_dir>/usr/bin/bcl-convert` in the same folder where the Dockerfile lies.
+3. Create and test the container:
+
+   ```bash
+   docker build . -t nfcore/bclconvert:<VERSION>
+   ```
+
+4. Access rights are needed to push the container to the Dockerhub nfcore organization, please ask a core team member to do so.
+
+   ```bash
+   docker push nfcore/bclconvert:<VERSION>
+   ```

modules/bclconvert/main.nf

@@ -0,0 +1,81 @@
+process BCLCONVERT {
+    tag '$samplesheet'
+    label 'process_high'
+
+    if (params.enable_conda) {
+        exit 1, "Conda environments cannot be used when using bcl-convert. Please use docker or singularity containers."
+    }
+    container "nfcore/bclconvert:3.9.3"
+
+    input:
+    path samplesheet
+    path run_dir
+
+    output:
+    path "*.fastq.gz"               ,emit: fastq
+    path "Reports/*.{csv,xml,bin}"  ,emit: reports
+    path "Logs/*.{log,txt}"         ,emit: logs
+    path "InterOp/*.bin"            ,emit: interop
+    path "versions.yml"             ,emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+
+    """
+    bcl-convert \
+        $args \\
+        --output-directory . \\
+        --bcl-input-directory ${run_dir} \\
+        --sample-sheet ${samplesheet} \\
+        --bcl-num-parallel-tiles ${task.cpus}
+
+    mkdir InterOp
+    cp ${run_dir}/InterOp/*.bin InterOp/
+    mv Reports/*.bin InterOp/
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bclconvert: \$(bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //')
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    echo "sample1_S1_L001_R1_001" > sample1_S1_L001_R1_001.fastq.gz
+    echo "sample1_S1_L001_R2_001" > sample1_S1_L001_R2_001.fastq.gz
+    echo "sample1_S1_L002_R1_001" > sample1_S1_L002_R1_001.fastq.gz
+    echo "sample1_S1_L002_R2_001" > sample1_S1_L002_R2_001.fastq.gz
+    echo "sample2_S2_L001_R1_001" > sample2_S2_L001_R1_001.fastq.gz
+    echo "sample2_S2_L001_R2_001" > sample2_S2_L001_R2_001.fastq.gz
+    echo "sample2_S2_L002_R1_001" > sample2_S2_L002_R1_001.fastq.gz
+    echo "sample2_S2_L002_R2_001" > sample2_S2_L002_R2_001.fastq.gz
+
+    mkdir Reports
+    echo "Adapter_Metrics" >  Reports/Adapter_Metrics.csv
+    echo "Demultiplex_Stats" >  Reports/Demultiplex_Stats.csv
+    echo "fastq_list" >  Reports/fastq_list.csv
+    echo "Index_Hopping_Counts" >  Reports/Index_Hopping_Counts.csv
+    echo "IndexMetricsOut" >  Reports/IndexMetricsOut.bin
+    echo "Quality_Metrics" >  Reports/Quality_Metrics.csv
+    echo "RunInfo" >  Reports/RunInfo.xml
+    echo "SampleSheet" >  Reports/SampleSheet.csv
+    echo "Top_Unknown_Barcodes" >  Reports/Top_Unknown_Barcodes.csv
+
+    mkdir Logs
+    echo "Errors" > Logs/Errors.log
+    echo "FastqComplete" > Logs/FastqComplete.txt
+    echo "Info" > Logs/Info.log
+    echo "Warnings" > Logs/Warnings.log
+
+    mkdir InterOp/
+    echo "InterOp" > InterOp/InterOp.bin
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bclconvert: \$(bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //')
+    END_VERSIONS
+    """
+}

modules/bclconvert/meta.yml

@@ -0,0 +1,45 @@
+name: "bclconvert"
+description: Demultiplex Illumina BCL files
+keywords:
+  - demultiplex
+  - illumina
+  - fastq
+tools:
+  - "bclconvert":
+      description: "Demultiplex Illumina BCL files"
+      homepage: "https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html"
+      documentation: "https://support-docs.illumina.com/SW/BCL_Convert/Content/SW/FrontPages/BCL_Convert.htm"
+      licence: "ILLUMINA"
+
+input:
+  - samplesheet:
+      type: file
+      description: "Input samplesheet"
+      pattern: "*.{csv}"
+  - run_dir:
+      type: directory
+      description: "Input run directory containing RunInfo.xml and BCL data"
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - fastq:
+      type: file
+      description: Demultiplexed FASTQ files
+      pattern: "*.{fastq.gz}"
+  - reports:
+      type: file
+      description: Demultiplexing Reports
+      pattern: "Reports/*.{csv,xml}"
+  - logs:
+      type: file
+      description: Log files
+      pattern: "Logs/*.{log,txt}"
+  - interop:
+      type: file
+      description: Interop files
+      pattern: "Interop/*.{bin}"
+authors:
+  - "@matthdsm"

tests/config/pytest_modules.yml

@@ -174,6 +174,10 @@ bcftools/view:
   - modules/bcftools/view/**
   - tests/modules/bcftools/view/**
 
+bclconvert:
+  - modules/bclconvert/**
+  - tests/modules/bclconvert/**
+
 bedtools/bamtobed:
   - modules/bedtools/bamtobed/**
   - tests/modules/bedtools/bamtobed/**

tests/modules/bclconvert/main.nf

@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BCLCONVERT } from '../../../modules/bclconvert/main.nf'
+
+process STUB_BCLCONVERT_INPUT {
+    output:
+    path "SampleSheet.csv"          ,emit: samplesheet
+    path "DDMMYY_SERIAL_FLOWCELL"   ,emit: run_dir
+
+    stub:
+    """
+    mkdir DDMMYY_SERIAL_FLOWCELL
+    echo "SampleSheet" > SampleSheet.csv
+    """
+}
+
+workflow test_bclconvert {
+    STUB_BCLCONVERT_INPUT ()
+    BCLCONVERT (STUB_BCLCONVERT_INPUT.out.samplesheet, STUB_BCLCONVERT_INPUT.out.run_dir)
+}

tests/modules/bclconvert/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}

tests/modules/bclconvert/test.yml

@@ -0,0 +1,52 @@
+- name: bclconvert test_bclconvert
+  command: nextflow run tests/modules/bclconvert -entry test_bclconvert -c tests/config/nextflow.config -stub-run
+  tags:
+    - bclconvert
+  files:
+    - path: output/bclconvert/InterOp/InterOp.bin
+      md5sum: d3dea0bb4ab1c8754af324f40b001481
+    - path: output/bclconvert/Logs/Errors.log
+      md5sum: 334645f09074b2597a692e395b716a9c
+    - path: output/bclconvert/Logs/FastqComplete.txt
+      md5sum: a4c4c6ce2d0de67d3b7ac7d1fcb512e4
+    - path: output/bclconvert/Logs/Info.log
+      md5sum: d238822d379f2277cac950ca986cb660
+    - path: output/bclconvert/Logs/Warnings.log
+      md5sum: aeefd2d631817e170f88f25ecaaf4664
+    - path: output/bclconvert/Reports/Adapter_Metrics.csv
+      md5sum: af62e9c7b44940cfd8ea11064a1f42ae
+    - path: output/bclconvert/Reports/Demultiplex_Stats.csv
+      md5sum: d11313931fcaabb5ce159462ad3dd1da
+    - path: output/bclconvert/Reports/IndexMetricsOut.bin
+      md5sum: 6bcee11c8145e3b1059ceaa91d2f5be7
+    - path: output/bclconvert/Reports/Index_Hopping_Counts.csv
+      md5sum: 697e40e0c0d48b4bd25f138ef60b0bde
+    - path: output/bclconvert/Reports/Quality_Metrics.csv
+      md5sum: 3902fd38f6b01f1ce0f0e8724238f8f2
+    - path: output/bclconvert/Reports/RunInfo.xml
+      md5sum: 5bef7c7e76360231b0c4afdfc915fd44
+    - path: output/bclconvert/Reports/SampleSheet.csv
+      md5sum: c579e7d2c9c917c4cfb875a0373c0936
+    - path: output/bclconvert/Reports/Top_Unknown_Barcodes.csv
+      md5sum: 39a5e7f6d21c12d6051afdc8261b6330
+    - path: output/bclconvert/Reports/fastq_list.csv
+      md5sum: 32c51ab10e013fd547928de57361ffcb
+    - path: output/bclconvert/sample1_S1_L001_R1_001.fastq.gz
+      md5sum: 9b831a39755935333f86f167527a094d
+    - path: output/bclconvert/sample1_S1_L001_R2_001.fastq.gz
+      md5sum: 082f4f767b7619f409ca7e752ef482bf
+    - path: output/bclconvert/sample1_S1_L002_R1_001.fastq.gz
+      md5sum: 837764c89db93dfb53cd663c4f26f3d7
+    - path: output/bclconvert/sample1_S1_L002_R2_001.fastq.gz
+      md5sum: 1a42cf6ba0bb8fc7770f278e6d1ab676
+    - path: output/bclconvert/sample2_S2_L001_R1_001.fastq.gz
+      md5sum: 475bc426b7cc48d0551d40e31457dc78
+    - path: output/bclconvert/sample2_S2_L001_R2_001.fastq.gz
+      md5sum: f670ccd7d9352e0e67fe1c1232429d94
+    - path: output/bclconvert/sample2_S2_L002_R1_001.fastq.gz
+      md5sum: ebd5ff6fa5603e7d704b5a10598de58c
+    - path: output/bclconvert/sample2_S2_L002_R2_001.fastq.gz
+      md5sum: 2f83b460f52620d2548c7ef8845b31d7
+    - path: output/stub/SampleSheet.csv
+      md5sum: c579e7d2c9c917c4cfb875a0373c0936
+    - path: output/bclconvert/versions.yml