Merge pull request #202 from MaxUlysse/save_bam_mapped

--save_bam_mapped works for every settings

CHANGELOG.md

@@ -28,7 +28,7 @@ Piellorieppe is one of the main massif in the Sarek National Park.
 - [#180](https://github.com/nf-core/sarek/pull/180) - Now saving Mapped BAMs (and creating TSV) in minimal setting
 - [#182](https://github.com/nf-core/sarek/pull/182) - Add possibility to run `HaplotypeCaller` without `dbsnp` so it can be used to actually generate vcfs to build a set of known sites (cf [gatkforums](https://gatkforums.broadinstitute.org/gatk/discussion/1247/what-should-i-use-as-known-variants-sites-for-running-tool-x))
 - [#195](https://github.com/nf-core/sarek/pull/195) - Now creating TSV for duplicates marked BAMs in minimal setting
-- [#195](https://github.com/nf-core/sarek/pull/195) - Add `--save_bam_mapped` params to save mapped BAMs.
+- [#195](https://github.com/nf-core/sarek/pull/195), [#202](https://github.com/nf-core/sarek/pull/202) - Add `--save_bam_mapped` params to save mapped BAMs.
 - [#197](https://github.com/nf-core/sarek/pull/197) - Add step `prepare_recalibration` to allow restart from DuplicatesMarked BAMs
 
 ### Changed

main.nf

@@ -1239,7 +1239,7 @@ process IndexBamFile {
     publishDir params.outdir, mode: params.publish_dir_mode,
         saveAs: {
             if (params.save_bam_mapped) "Preprocessing/${idSample}/Mapped/${it}"
-            null
+            else null
         }
 
     input:
@@ -1249,7 +1249,7 @@ process IndexBamFile {
         set idPatient, idSample, file("${idSample}.bam"), file("${idSample}.bam.bai") into bam_mapped_merged_indexed
         set idPatient, idSample into tsv_bam_indexed
 
-    when: !(params.known_indels)
+    when: params.save_bam_mapped || !(params.known_indels)
 
     script:
     """
@@ -2136,8 +2136,6 @@ vcfMantaSingle = vcfMantaSingle.dump(tag:'Single Manta')
 process TIDDIT {
     tag {idSample}
 
-    publishDir "${params.outdir}/VariantCalling/${idSample}/TIDDIT", mode: params.publish_dir_mode
-
     publishDir params.outdir, mode: params.publish_dir_mode,
         saveAs: {
             if (it == "TIDDIT_${idSample}.vcf") "VariantCalling/${idSample}/TIDDIT/${it}"
@@ -2812,7 +2810,7 @@ process MSIsensor_msi {
 
     tag {idSampleTumor + "_vs_" + idSampleNormal}
 
-    publishDir "${params.outdir}/VariantCalling/${idSampleTumor}_vs_${idSampleNormal}/MSIsensor", mode: params.publishDirMode
+    publishDir "${params.outdir}/VariantCalling/${idSampleTumor}_vs_${idSampleNormal}/MSIsensor", mode: params.publish_dir_mode
 
     input:
         set idPatient, idSampleNormal, file(bamNormal), file(baiNormal), idSampleTumor, file(bamTumor), file(baiTumor) from pairBamMsisensor