[POC] Get subworkflows working again - bam_stats_samtools (#2097)

* [POC] Get subworkflows working again - bam_stats_samtools

* Comment out aliased anchors

* Add explicit anchor to pytest_modules.yml

* test(subworkflows): Remove anchors

There are two options to get the tests to trigger:

1. Add the module anchors to the subworkflows (less things to update and maintain because we only have to update the module triggers)

2. Add the tags to the pytest workflow spec.

This is option 2.

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

subworkflows/nf-core/bam_stats_samtools/main.nf

@@ -2,26 +2,25 @@
 // Run SAMtools stats, flagstat and idxstats
 //
 
-params.options = [:]
-
-include { SAMTOOLS_STATS    } from '../../../modules/samtools/stats/main'    addParams( options: params.options )
-include { SAMTOOLS_IDXSTATS } from '../../../modules/samtools/idxstats/main' addParams( options: params.options )
-include { SAMTOOLS_FLAGSTAT } from '../../../modules/samtools/flagstat/main' addParams( options: params.options )
+include { SAMTOOLS_STATS    } from '../../../modules/samtools/stats/main'
+include { SAMTOOLS_IDXSTATS } from '../../../modules/samtools/idxstats/main'
+include { SAMTOOLS_FLAGSTAT } from '../../../modules/samtools/flagstat/main'
 
 workflow BAM_STATS_SAMTOOLS {
     take:
-    ch_bam_bai // channel: [ val(meta), [ bam ], [bai/csi] ]
+    bam_bai // channel: [ val(meta), [ bam/cram ], [bai/csi] ]
+    fasta   // channel: [ fasta ]
 
     main:
     ch_versions = Channel.empty()
 
-    SAMTOOLS_STATS ( ch_bam_bai, [] )
+    SAMTOOLS_STATS ( bam_bai, fasta )
     ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions.first())
 
-    SAMTOOLS_FLAGSTAT ( ch_bam_bai )
+    SAMTOOLS_FLAGSTAT ( bam_bai )
     ch_versions = ch_versions.mix(SAMTOOLS_FLAGSTAT.out.versions.first())
 
-    SAMTOOLS_IDXSTATS ( ch_bam_bai )
+    SAMTOOLS_IDXSTATS ( bam_bai )
     ch_versions = ch_versions.mix(SAMTOOLS_IDXSTATS.out.versions.first())
 
     emit:

subworkflows/nf-core/bam_stats_samtools/meta.yml

@@ -1,4 +1,4 @@
-name: samtools_stats
+name: bam_stats_samtools
 description: Produces comprehensive statistics from SAM/BAM/CRAM file
 keywords:
   - statistics
@@ -24,6 +24,10 @@ input:
       type: file
       description: Index for BAM/CRAM/SAM file
       pattern: "*.{bai,crai,sai}"
+  - fasta:
+      type: file
+      description: Reference genome fasta file
+      pattern: "*.{fasta,fa}"
 # TODO Update when we decide on a standard for subworkflow docs
 output:
   - meta:
@@ -35,6 +39,14 @@ output:
       type: file
       description: File containing samtools stats output
       pattern: "*.{stats}"
+  - flagstat:
+      type: file
+      description: File containing samtools flagstat output
+      pattern: "*.{flagstat}"
+  - idxstats:
+      type: file
+      description: File containing samtools idxstats output
+      pattern: "*.{idxstats}"
   - versions:
       type: file
       description: File containing software versions

subworkflows/nf-core/bam_stats_samtools/nextflow.config

@@ -1 +0,0 @@
-params.options = [:]

tests/config/pytest_modules.yml

@@ -2355,6 +2355,10 @@ subread/featurecounts:
   - modules/subread/featurecounts/**
   - tests/modules/subread/featurecounts/**
 
+subworkflows/bam_stats_samtools:
+  - subworkflows/nf-core/bam_stats_samtools/**
+  - tests/subworkflows/nf-core/bam_stats_samtools/**
+
 svdb/merge:
   - modules/svdb/merge/**
   - tests/modules/svdb/merge/**

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

@@ -2,22 +2,27 @@
 
 nextflow.enable.dsl = 2
 
-include { BAM_STATS_SAMTOOLS } from '../../../../subworkflows/nf-core/bam_stats_samtools/main' addParams( options: [:] )
+include { BAM_STATS_SAMTOOLS as BAM_STATS_SAMTOOLS_SINGLE_END } from '../../../../subworkflows/nf-core/bam_stats_samtools/main'
+include { BAM_STATS_SAMTOOLS as BAM_STATS_SAMTOOLS_PAIRED_END } from '../../../../subworkflows/nf-core/bam_stats_samtools/main'
 
 workflow test_bam_stats_samtools_single_end {
-    input = [ [ id:'test', single_end:false ], // meta map
-             file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
-             file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true)
+    input = [ 
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true)
     ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
-    BAM_STATS_SAMTOOLS ( input )
+    BAM_STATS_SAMTOOLS_SINGLE_END ( input, fasta )
 }
 
 workflow test_bam_stats_samtools_paired_end {
-    input = [ [ id:'test', single_end:false ], // meta map
-             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)
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        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)
     ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
-    BAM_STATS_SAMTOOLS ( input )
+    BAM_STATS_SAMTOOLS_PAIRED_END ( input, fasta )
 }

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

@@ -0,0 +1,13 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: '.*:BAM_STATS_SAMTOOLS_SINGLE_END:.*' {
+        ext.prefix = { "${meta.id}.single_end.sorted.bam" }
+    }
+
+    withName: '.*:BAM_STATS_SAMTOOLS_PAIRED_END:.*' {
+        ext.prefix = { "${meta.id}.paired_end.sorted.bam" }
+    }
+
+}

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

@@ -1,13 +1,14 @@
 - name: bam stats samtools single-end
-  command: nextflow run ./tests/subworkflows/nf-core/bam_stats_samtools -entry test_bam_stats_samtools_single_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/subworkflows/nf-core/bam_stats_samtools -entry test_bam_stats_samtools_single_end -c ./tests/config/nextflow.config -c ./tests/subworkflows/nf-core/bam_stats_samtools/nextflow.config
   tags:
     - subworkflows
-    # - subworkflows/bam_stats_samtools
+    - subworkflows/bam_stats_samtools
+    - bam_stats_samtools
     # Modules
-    # - samtools
-    # - samtools/stats
-    # - samtools/idxstats
-    # - samtools/flagstat
+    - samtools
+    - samtools/stats
+    - samtools/idxstats
+    - samtools/flagstat
   files:
     - path: ./output/samtools/test.single_end.sorted.bam.flagstat
       md5sum: 2191911d72575a2358b08b1df64ccb53
@@ -16,15 +17,16 @@
     - path: ./output/samtools/test.single_end.sorted.bam.stats
 
 - name: bam stats samtools paired-end
-  command: nextflow run ./tests/subworkflows/nf-core/bam_stats_samtools -entry test_bam_stats_samtools_paired_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/subworkflows/nf-core/bam_stats_samtools -entry test_bam_stats_samtools_paired_end -c ./tests/config/nextflow.config -c ./tests/subworkflows/nf-core/bam_stats_samtools/nextflow.config
   tags:
     - subworkflows
-    # - subworkflows/bam_stats_samtools
-    # # Modules
-    # - samtools
-    # - samtools/stats
-    # - samtools/idxstats
-    # - samtools/flagstat
+    - subworkflows/bam_stats_samtools
+    - bam_stats_samtools
+    # Modules
+    - samtools
+    - samtools/stats
+    - samtools/idxstats
+    - samtools/flagstat
   files:
     - path: ./output/samtools/test.paired_end.sorted.bam.flagstat
       md5sum: 4f7ffd1e6a5e85524d443209ac97d783