Merge branch 'dev' into test-full-fix

Author: jfy133

.github/workflows/ci.yml

@@ -201,6 +201,10 @@ jobs:
       - name: METAGENOMIC Run the basic pipeline but with unmapped reads going into Kraken
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_kraken,docker --run_bam_filtering  --bam_unmapped_type 'fastq'
+      - name: SNPCAPTURE Run the basic pipeline with the bam input profile, generating statistics with a SNP capture bed
+        run: |
+          wget https://github.com/nf-core/test-datasets/raw/eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz && gunzip 1240K.pos.list_hs37d5.0based.bed.gz
+          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_humanbam,docker --skip_fastqc --skip_adapterremoval --skip_deduplication --snpcapture_bed 1240K.pos.list_hs37d5.0based.bed
       - name: SEXDETERMINATION Run the basic pipeline with the bam input profile, but don't convert BAM, skip everything but sex determination
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_humanbam,docker --skip_fastqc --skip_adapterremoval --skip_deduplication --skip_qualimap --run_sexdeterrmine

CHANGELOG.md

@@ -10,6 +10,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### `Fixed`
 
 - [#836](https://github.com/nf-core/eager/issues/836) Remove deprecated parameters from test profiles
+- [#838](https://github.com/nf-core/eager/issues/836) Fix --snpcapture_bed files not being picked up by Nextflow
+- Fix PMDtools reference mask not being picked up by Nextflow, and it's use being evaluated against --snpcapture_bed rather than --pmdtools_reference_mask
 
 ### `Dependencies`
 

main.nf

@@ -245,6 +245,17 @@ if ( !params.clip_adapters_list ) {
       .set {ch_adapterlist}
 }
 
+if ( params.snpcapture_bed ) {
+    Channel.fromPath(params.snpcapture_bed, checkIfExists: true).into { ch_snpcapture_bed; ch_snpcapture_bed_pmd }
+} else {
+    Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt").into { ch_snpcapture_bed; ch_snpcapture_bed_pmd }
+}
+
+if ( params.pmdtools_reference_mask ) {
+    ch_pmdtoolsmask = Channel.fromPath(params.pmdtools_reference_mask, checkIfExists: true)
+} else {
+    ch_pmdtoolsmask = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy2.txt")
+}
 
 // SexDetermination channel set up and bedfile validation
 if (!params.sexdeterrmine_bedfile) {
@@ -2137,6 +2148,8 @@ process pmdtools {
     input: 
     tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path(bam), path(bai) from ch_rmdup_for_pmdtools
     file fasta from ch_fasta_for_pmdtools.collect()
+    path snpcapture_bed from ch_snpcapture_bed_pmd
+    path pmdtools_reference_mask from ch_pmdtoolsmask
 
     output:
     tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*.pmd.bam"), path("*.pmd.bam.{bai,csi}") into ch_output_from_pmdtools
@@ -2145,12 +2158,8 @@ process pmdtools {
     script:
     //Check which treatment for the libraries was used
     def treatment = udg ? (udg == 'half' ? '--UDGhalf' : '--CpG') : '--UDGminus'
-    if(params.snpcapture_bed){
-        snpcap = (params.pmdtools_reference_mask) ? "--refseq ${params.pmdtools_reference_mask}" : ''
-        log.info"######No reference mask specified for PMDtools, therefore ignoring that for downstream analysis!"
-    } else {
-        snpcap = ''
-    }
+    def snpcap = snpcapture_bed.getName() != 'nf-core_eager_dummy.txt' ? "--refseq ${pmdtools_reference_mask} --basecomposition" : ''
+    if ( snpcapture_bed.getName() != 'nf-core_eager_dummy.txt' && !params.pmdtools_reference_mask ) { log.info "[nf-core/eager] warn: No reference mask specified for PMDtools, therefore ignoring that for downstream analysis!" }
     def size = params.large_ref ? '-c' : ''
     def platypus = params.pmdtools_platypus ? '--platypus' : ''
     """
@@ -2281,12 +2290,13 @@ process qualimap {
     input:
     tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path(bam), path(bai) from ch_addlibmerge_for_qualimap
     file fasta from ch_fasta_for_qualimap.collect()
+    path snpcapture_bed from ch_snpcapture_bed 
 
     output:
     tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*") into ch_qualimap_results
 
     script:
-    def snpcap = params.snpcapture_bed ? "-gff ${params.snpcapture_bed}" : ''
+    def snpcap = snpcapture_bed.getName() != 'nf-core_eager_dummy.txt' ? "-gff ${snpcapture_bed}" : ''
     """
     qualimap bamqc -bam $bam -nt ${task.cpus} -outdir . -outformat "HTML" ${snpcap} --java-mem-size=${task.memory.toGiga()}G
     """