New Subworkflow: Bam_trim_primers_ivar

subworkflows/nf-core/bam_trim_primers_ivar/main.nf

@@ -0,0 +1,44 @@
+include { IVAR_TRIM               } from '../../../modules/nf-core/ivar/trim/main'
+include { BAM_SORT_STATS_SAMTOOLS } from '../bam_sort_stats_samtools/main'
+
+workflow BAM_TRIM_PRIMERS_IVAR {
+    take:
+    ch_bam   // channel: [ val(meta), path(bam), path(bai) ]
+    ch_bed   // channel: [ path(bed) ]
+    ch_fasta // channel: [ path(fasta) ]
+
+    main:
+    ch_versions = Channel.empty()
+
+    //
+    // iVar trim primers
+    //
+    IVAR_TRIM (
+        ch_bam,
+        ch_bed
+    )
+    ch_versions = ch_versions.mix(IVAR_TRIM.out.versions.first())
+
+    //
+    // Sort, index BAM file and run samtools stats, flagstat and idxstats
+    //
+    BAM_SORT_STATS_SAMTOOLS (
+        IVAR_TRIM.out.bam,
+        ch_fasta
+    )
+
+    ch_versions = ch_versions.mix(BAM_SORT_STATS_SAMTOOLS.out.versions.first())
+
+    emit:
+    bam_orig = IVAR_TRIM.out.bam                    // channel: [ val(meta), path(bam) ]
+    log_out  = IVAR_TRIM.out.log                    // channel: [ val(meta), path(log) ]
+
+    bam      = BAM_SORT_STATS_SAMTOOLS.out.bam      // channel: [ val(meta), path(bam) ]
+    bai      = BAM_SORT_STATS_SAMTOOLS.out.bai      // channel: [ val(meta), path(bai) ]
+    csi      = BAM_SORT_STATS_SAMTOOLS.out.csi      // channel: [ val(meta), path(csi) ]
+    stats    = BAM_SORT_STATS_SAMTOOLS.out.stats    // channel: [ val(meta), path(stats) ]
+    flagstat = BAM_SORT_STATS_SAMTOOLS.out.flagstat // channel: [ val(meta), path(flagstat) ]
+    idxstats = BAM_SORT_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), path(idxstats) ]
+
+    versions = ch_versions                          // channel: [ path(versions.yml) ]
+}

subworkflows/nf-core/bam_trim_primers_ivar/meta.yml

@@ -0,0 +1,102 @@
+name: "bam_trim_primers_ivar"
+description: Trim primers using IVAR tools and perform summary statistics.
+keywords:
+  - amplicon sequencing
+  - trimming
+  - ivar
+  - fasta
+  - sort
+  - bam
+  - sam
+  - cram
+
+modules:
+  - ivar/trim
+  - samtools/sort
+  - samtools/index
+  - samtools/stats
+  - samtools/idxstats
+  - samtools/flagstat
+
+tools:
+  - ivar:
+      description: |
+        iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.
+      homepage: https://github.com/andersen-lab/ivar
+      documentation: https://andersen-lab.github.io/ivar/html/manualpage.html
+      licence: ["GPL-3.0-or-later"]
+
+input:
+  - ch_bam:
+      type: file
+      description: |
+        Structure: [ val(meta), path(bam), path(bai) ]
+        Groovy Map containing sample information
+        e.g. [ id:'test' ], BAM/CRAM/SAM file, index file for co-ordinate sorted BAM file
+  - ch_bed:
+      type: file
+      description: |
+        Structure: path(bed)
+        BED file with primer labels and positions
+      pattern: "*.bed"
+  - ch_fasta:
+      type: file
+      description: |
+        Structure: path(fasta)
+        Reference genome fasta file
+      pattern: "*.{fasta,fa}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam_org:
+      type: file
+      description: |
+        Structure: [ val(meta), path(bam) ]
+        iVar generated trimmed bam file (unsorted)
+  - log_out:
+      type: file
+      description: |
+        Structure: [ val(meta), path(log) ]
+        Log file generated by iVar for use with MultiQC
+      pattern: "*.log"
+
+  - bam:
+      type: file
+      description: |
+        Structure: [ val(meta), path(bam) ]
+        Sorted BAM/CRAM/SAM file
+  - bai:
+      type: file
+      description: |
+        Structure: [ val(meta), path(bai) ]
+        BAM/CRAM/SAM index file
+  - crai:
+      type: file
+      description: |
+        Structure: [ val(meta), path(crai) ]
+        BAM/CRAM/SAM index file
+  - stats:
+      type: file
+      description: |
+        Structure: [ val(meta), path(stats) ]
+        File containing samtools stats output
+  - flagstat:
+      type: file
+      description: |
+        Structure: [ val(meta), path(flagstat) ]
+        File containing samtools flagstat output
+  - idxstats:
+      type: file
+      description: |
+        Structure: [ val(meta), path(idxstats) ]
+        File containing samtools idxstats output
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@Joon-Klaps"

tests/config/pytest_modules.yml

@@ -1885,6 +1885,9 @@ subworkflows/bam_sort_samtools:
 subworkflows/bam_split_by_region:
   - subworkflows/nf-core/bam_split_by_region/**
   - tests/subworkflows/nf-core/bam_split_by_region/**
+subworkflows/bam_trim_primers_ivar:
+  - subworkflows/nf-core/bam_trim_primers_ivar/**
+  - tests/subworkflows/nf-core/bam_trim_primers_ivar/**
 subworkflows/bam_tumor_normal_somatic_variant_calling_gatk:
   - subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_gatk/**
   - tests/subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_gatk/**

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

@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BAM_TRIM_PRIMERS_IVAR } from '../../../../subworkflows/nf-core/bam_trim_primers_ivar/main.nf'
+
+workflow test_bam_trim_primers_ivar {
+
+    input = [
+        [ id:'test'],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+            ]
+    bed_file   = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BAM_TRIM_PRIMERS_IVAR ( input, bed_file, fasta )
+}

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

@@ -0,0 +1,12 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: '.*:SAMTOOLS_.*' {
+        ext.prefix = { "${meta.id}.paired_end.sorted" }
+    }
+
+    withName: '.*:BAM_STATS_SAMTOOLS:.*' {
+        ext.prefix = { "${meta.id}.paired_end.sorted.bam" }
+    }
+}

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

@@ -0,0 +1,16 @@
+- name: bam_trim_primers_ivar test_bam_trim_primers_ivar
+  command: nextflow run ./tests/subworkflows/nf-core/bam_trim_primers_ivar -entry test_bam_trim_primers_ivar -c ./tests/config/nextflow.config
+  tags:
+    - ivar
+    - ivar/trim
+    - subworkflows
+    - subworkflows/bam_sort_stats_samtools
+    - subworkflows/bam_trim_primers_ivar
+  files:
+    - path: output/ivar/test.bam
+    - path: output/ivar/test.ivar.log
+    - path: output/samtools/test.paired_end.sorted.bam
+    - path: output/samtools/test.paired_end.sorted.bam.bai
+    - path: output/samtools/test.paired_end.sorted.bam.flagstat
+    - path: output/samtools/test.paired_end.sorted.bam.idxstats
+    - path: output/samtools/test.paired_end.sorted.bam.stats