Feature/extractumi

install_data.sh

@@ -0,0 +1,27 @@
+#!/usr/bin/env bash
+
+
+# Test data is hosted on Google Drive at:
+# https://drive.google.com/file/d/1GtT8jsBGwRoQC-5wHh06r8RFkiFBuirp/view?usp=sharing
+
+fileid=1GtT8jsBGwRoQC-5wHh06r8RFkiFBuirp
+
+filename=test_nucleo.tar.gz
+foldername=test_nucleo
+
+# Skip if already have test data
+[[ -f $filename ]] && exit 0
+[[ -d $foldername ]] && exit 0
+
+curl -c ./cookie -s -k -L "https://drive.google.com/uc?export=download&id=$fileid" > /dev/null
+
+curl -k -Lb ./cookie "https://drive.google.com/uc?export=download&confirm=`awk '/download/ {print $NF}' ./cookie`&id=${fileid}" -o ${filename}
+
+# Suppress linux warnings for MacOS tar.gz files
+if [[ "$OSTYPE" == "linux-gnu" ]]; then
+    tar --warning=no-unknown-keyword -xzvf $filename
+elif [[ "$OSTYPE" == "darwin"* ]]; then
+    tar -xzvf $filename
+fi
+
+rm $filename

subworkflows/nf-core/fastq_extractumi_fgbio_picard_gatk4_fastp/main.nf

@@ -0,0 +1,68 @@
+// TODO nf-core: If in doubt look at other nf-core/subworkflows to see how we are doing things! :)
+//               https://github.com/nf-core/modules/tree/master/subworkflows
+//               You can also ask for help via your pull request or on the #subworkflows channel on the nf-core Slack workspace:
+//               https://nf-co.re/join
+// TODO nf-core: A subworkflow SHOULD import at least two modules
+
+include { FGBIO_FASTQTOBAM } from '../../../modules/nf-core/fgbio/fastqtobam/main'
+include { PICARD_MERGESAMFILES } from '../../../modules/nf-core/picard/mergesamfiles/'
+include { GATK4_SAMTOFASTQ } from '../../../modules/nf-core/gatk4/samtofastq/main'
+include { FASTP } from '../../../modules/nf-core/fastp/main'
+
+workflow FASTQ_EXTRACTUMI_FGBIO_PICARD_GATK4_FASTP {
+
+    take:
+    // TODO nf-core: edit input (take) channels
+    ch_fastq // channel: [ val(meta), [ bam ] ]
+
+    main:
+
+    ch_versions = Channel.empty()
+
+    // FGBIO_FASTQTOBAM: get unmerged bams
+    // ch_fastq is a channel, which enables parallel
+    // channels enable parallel: https://www.nextflow.io/docs/latest/faq.html?highlight=parallel
+    FGBIO_FASTQTOBAM (
+        ch_fastq
+    )
+    FGBIO_FASTQTOBAM.out.bam.map{
+        meta, bam ->
+            [bam]
+    }.collect().map{
+        bams ->
+        [[id: 'unmerged_bams'], bams ]
+    }.set{unmerged_bams}
+    ch_versions = ch_versions.mix(FGBIO_FASTQTOBAM.out.versions) //write out versioning
+
+    // PICARD_MERGESAMFILES: merge bams files
+    PICARD_MERGESAMFILES (
+        unmerged_bams
+    ).bam.map {
+        meta, bam ->
+            new_id = 'merged_bam'
+            [[id: new_id], bam ]
+    }.set {merged_bam}
+    ch_versions = ch_versions.mix(PICARD_MERGESAMFILES.out.versions)
+    // GATK4_SAMTOFASTQ: get fastqs from merged bam
+    GATK4_SAMTOFASTQ (
+        merged_bam
+    ).fastq.map {
+        meta, fastq ->
+            new_id = 'merged_fastq'
+            [[id: new_id], fastq ]
+    }.set {merged_fastq}
+    ch_versions = ch_versions.mix(GATK4_SAMTOFASTQ.out.versions)
+
+    // GATK4_SAMTOFASTQ: Run fastp on fastqs
+    FASTP (
+        merged_fastq, [], false, false
+    )
+    ch_versions = ch_versions.mix(FASTP.out.versions)
+    // final emit
+    emit:
+    // TODO nf-core: edit emitted channels
+    bam = FASTP.out.reads
+
+    versions = ch_versions                     // channel: [ versions.yml ]
+
+}

subworkflows/nf-core/fastq_extractumi_fgbio_picard_gatk4_fastp/meta.yml

@@ -0,0 +1,48 @@
+name: "fastq_extractumi_fgbio_picard_gatk4_fastp"
+## TODO nf-core: Add a description of the subworkflow and list keywords
+description: Sort SAM/BAM/CRAM file
+keywords:
+  - sort
+  - bam
+  - sam
+  - cram
+## TODO nf-core: Add a list of the modules used in the subworkflow
+modules:
+  - samtools/sort
+  - samtools/index
+## TODO nf-core: List all of the variables used as input, including their types and descriptions
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - bam:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+## TODO nf-core: List all of the variables used as output, including their types and descriptions
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - bam:
+      type: file
+      description: Sorted BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+  - bai:
+      type: file
+      description: BAM/CRAM/SAM samtools index
+      pattern: "*.{bai,crai,sai}"
+  - csi:
+      type: file
+      description: CSI samtools index
+      pattern: "*.csi"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@buehlere"

tests/config/pytest_modules.yml

@@ -3736,6 +3736,10 @@ subworkflows/fastq_download_prefetch_fasterqdump_sratools:
   - subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/**
   - tests/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/**
 
+subworkflows/fastq_extractumi_fgbio_picard_gatk4_fastp:
+  - subworkflows/nf-core/fastq_extractumi_fgbio_picard_gatk4_fastp/**
+  - tests/subworkflows/nf-core/fastq_extractumi_fgbio_picard_gatk4_fastp/**
+
 subworkflows/fastq_fastqc_umitools_fastp:
   - subworkflows/nf-core/fastq_fastqc_umitools_fastp/**
   - tests/subworkflows/nf-core/fastq_fastqc_umitools_fastp/**

tests/subworkflows/nf-core/fastq_extractumi_fgbio_picard_gatk4_fastp/main.nf

@@ -0,0 +1,26 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { FASTQ_EXTRACTUMI_FGBIO_PICARD_GATK4_FASTP } from '../../../../subworkflows/nf-core/fastq_extractumi_fgbio_picard_gatk4_fastp/main.nf'
+
+
+workflow test_fastq_extractumi_fgbio_picard_gatk4_fastp {
+    // load test data
+    def bashScriptFile = new File('install_data.sh')
+
+    def processBuilder = new ProcessBuilder('bash', bashScriptFile.toString())
+    processBuilder.redirectOutput(ProcessBuilder.Redirect.INHERIT)
+    processBuilder.redirectError(ProcessBuilder.Redirect.INHERIT)
+
+    def process = processBuilder.start()
+    process.waitFor()
+
+    // channels enable parralle: https://www.nextflow.io/docs/latest/faq.html?highlight=parallel
+    fastq = [
+    [[id:'gene1', single_end:false], [file('test_nucleo/fastq/seracare_0-5_R1_001ad.fastq.gz'), file('test_nucleo/fastq/seracare_0-5_R2_001ad.fastq.gz')]],
+    [[id:'gene2', single_end:false], [file('test_nucleo/fastq/seracare_0-5_R1_001ae.fastq.gz'), file('test_nucleo/fastq/seracare_0-5_R2_001ae.fastq.gz')]]
+    ]
+    fastq = ch_fastq = Channel.fromList(fastq)
+    FASTQ_EXTRACTUMI_FGBIO_PICARD_GATK4_FASTP ( fastq )
+}

tests/subworkflows/nf-core/fastq_extractumi_fgbio_picard_gatk4_fastp/nextflow.config

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

tests/subworkflows/nf-core/fastq_extractumi_fgbio_picard_gatk4_fastp/test.yml

@@ -0,0 +1,27 @@
+- name: fastq_extractumi_fgbio_picard_gatk4_fastp test_fastq_extractumi_fgbio_picard_gatk4_fastp
+  command: nextflow run ./tests/subworkflows/nf-core/fastq_extractumi_fgbio_picard_gatk4_fastp -entry test_fastq_extractumi_fgbio_picard_gatk4_fastp -c ./tests/config/nextflow.config
+  tags:
+    - fastp
+    - fgbio
+    - fgbio/fastqtobam
+    - gatk4
+    - gatk4/samtofastq
+    - picard
+    - picard/mergesamfiles
+    - subworkflows
+    - subworkflows/fastq_extractumi_fgbio_picard_gatk4_fastp
+  files:
+    - path: output/bwa/bwa/chr14_chr16.amb
+      md5sum: 00fb74627e074db6238dcd9bc08dc48a
+    - path: output/bwa/bwa/chr14_chr16.ann
+      md5sum: d8825e2fcb3cd372cd61ededfe283025
+    - path: output/bwa/bwa/chr14_chr16.bwt
+      md5sum: 45637ec2c011d0f73cac6c470c5b5d2b
+    - path: output/bwa/bwa/chr14_chr16.pac
+      md5sum: 46f856371d59e859295497c967478d31
+    - path: output/bwa/bwa/chr14_chr16.sa
+      md5sum: 466dbbbce2fb9528e760477ccdc2ea5b
+    - path: output/bwa/gene.bam
+      md5sum: d7c5943b79704d8ed7f432786738f25d
+    - path: output/picard/aligned_bam.bam
+      md5sum: 89acecb9fcb99f9182a417215489ea50