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mapo9 · Apr 10, 2024 · 2a42c32 · 2a42c32
1 parent 6639f0f
commit 2a42c32
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Showing 3 changed files with 14 additions and 10 deletions.
diff --git a/modules/local/trust4.nf b/modules/local/trust4.nf
@@ -13,14 +13,16 @@ process TRUST4 {
     tuple val(meta3), path(vdj_reference)
 
     output:
-    tuple val(meta), path("*.tsv")              , emit: tsv
-    tuple val(meta), path("*_airr.tsv")         , emit: airr_files
-    tuple val(meta), path("${meta.id}_airr.tsv") , emit: airr_tsv
-    tuple val(meta), path("*_report.tsv")       , emit: report_tsv
-    tuple val(meta), path("*.fa")               , emit: fasta
-    tuple val(meta), path("*.out")              , emit: out
-    tuple val(meta), path("*.fq")               , emit: fq
-    path "versions.yml"                         , emit: versions
+    tuple val(meta), path("*.tsv")                          , emit: tsv
+    tuple val(meta), path("*_airr.tsv")                     , emit: airr_files
+    tuple val(meta), path("${meta.id}_airr.tsv")            , emit: airr_tsv
+    tuple val(meta), path("${meta.id}_barcode_airr.tsv")    , emit: barcode_airr
+    tuple val(meta), path("*_report.tsv")                   , emit: report_tsv
+    tuple val(meta), path("*.fa")                           , emit: fasta
+    tuple val(meta), path("*.out")                          , emit: out
+    tuple val(meta), path("*.fq")                           , emit: fq
+    tuple val(meta), path("**")                             , emit: outs
+    path "versions.yml"                                     , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/subworkflows/local/rnaseq_input.nf b/subworkflows/local/rnaseq_input.nf
@@ -64,8 +64,10 @@ workflow RNASEQ_INPUT {
     )
 
     ch_trust4_out = TRUST4.out.out
-    ch_trust4_airr = TRUST4.out.airr_tsv
+    //ch_trust4_airr = TRUST4.out.airr_tsv
+    ch_trust4_airr = TRUST4.out.barcode_airr
 
+    ch_trust4_airr.view()
     // rename tsv file to unique name
     RENAME_FILE_TSV(
                 ch_trust4_airr

diff --git a/subworkflows/local/sc_raw_input.nf b/subworkflows/local/sc_raw_input.nf
@@ -65,7 +65,7 @@ workflow SC_RAW_INPUT {
                 [ meta, out_files.find { it.endsWith("airr_rearrangement.tsv") } ]
             }
         .set { ch_cellranger_airr }
-
+    
     // TODO : add VALIDATE_INPUT Module
     // this module requires input in csv format... Might need to create this in an extra module