Merge branch 'cram_handling' into cram_handling

reichan1998 · Oct 1, 2024 · b089fa8 · b089fa8
2 parents 1e76d93 + c39bb79
commit b089fa8
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Showing 2 changed files with 10 additions and 3 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -12,6 +12,7 @@
 
 process {
     withName: SAMTOOLS_FASTQ {
+        beforeScript = { "export REF_PATH=spoof"}
         ext.args = '-F 0x200 -nt'
     }
 
@@ -20,6 +21,7 @@ process {
     }
 
     withName: SAMTOOLS_MERGE {
+        beforeScript = { "export REF_PATH=spoof"}
         ext.args = { "-c -p" }
         ext.prefix = { "${meta.id}.merge" }
     }
@@ -31,6 +33,7 @@ process {
     }
 
     withName: SAMTOOLS_COLLATETOFASTA {
+        beforeScript = { "export REF_PATH=spoof"}
         ext.args   = { (params.use_work_dir_as_temp ? "-T." : "") }
     }
 
@@ -39,6 +42,7 @@ process {
     }
 
     withName: SAMTOOLS_CONVERT {
+        beforeScript = { "export REF_PATH=spoof"}
         ext.args = "-be '[rq]>=0.99' -x fi -x fp -x ri -x rp --write-index"
     }
 
@@ -132,6 +136,7 @@ process {
     }
 
     withName: '.*:CONVERT_STATS:SAMTOOLS_CRAM' {
+        beforeScript = { "export REF_PATH=spoof"}
         ext.prefix = { "${fasta.baseName}.${meta.datatype}.${meta.id}" }
         ext.args   = '--output-fmt cram --write-index'
     }
@@ -155,6 +160,7 @@ process {
     }
 
     withName: SAMTOOLS_STATS {
+        beforeScript = { "export REF_PATH=spoof"}
         ext.prefix = { "${input.baseName}" }
     }
 
@@ -164,6 +170,7 @@ process {
     }
 
     withName: '.*:CONVERT_STATS:SAMTOOLS_.*' {
+        beforeScript = { "export REF_PATH=spoof"}
         publishDir = [
             path: { "${params.outdir}/read_mapping/${meta.datatype}" },
             mode: params.publish_dir_mode,

diff --git a/subworkflows/local/filter_pacbio.nf b/subworkflows/local/filter_pacbio.nf
@@ -9,7 +9,7 @@ include { BLAST_BLASTN                      } from '../../modules/nf-core/blast/
 include { PACBIO_FILTER                     } from '../../modules/local/pacbio_filter'
 include { SAMTOOLS_FILTERTOFASTQ            } from '../../modules/local/samtools_filtertofastq'
 include { SEQKIT_FQ2FA                      } from '../../modules/nf-core/seqkit/fq2fa'
-include { BBMAP_FILTERBYNAME                } from '../../modules/nf-core/bbmap/filterbyname/main'
+include { BBMAP_FILTERBYNAME               } from '../../modules/nf-core/bbmap/filterbyname'
 
 
 workflow FILTER_PACBIO {
@@ -67,7 +67,7 @@ workflow FILTER_PACBIO {
     ch_versions = ch_versions.mix ( PACBIO_FILTER.out.versions.first() )
 
 
-    // Filter the BAM files and convert to FASTQ
+    // Filter the input BAM and output as interleaved FASTA
     SAMTOOLS_CONVERT.out.bam
     | join ( SAMTOOLS_CONVERT.out.csi )
     | join ( PACBIO_FILTER.out.list )
@@ -81,7 +81,7 @@ workflow FILTER_PACBIO {
     ch_versions = ch_versions.mix ( SAMTOOLS_FILTERTOFASTQ.out.versions.first() )
 
 
-    // Filter inputs provided as FASTQ
+    // Filter inputs provided as FASTQ and output as interleaved FASTQ
     ch_reads.fastq
     | join(PACBIO_FILTER.out.list)
     | multiMap { meta, fastq, list -> \