reconnect to the overall workflow [ci skip]

TORCH-Consortium · Jun 23, 2024 · fd2082c · fd2082c
1 parent 4a2a04a
commit fd2082c
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Showing 3 changed files with 7 additions and 7 deletions.
diff --git a/bin/fastq_cohort_validation.py b/bin/fastq_cohort_validation.py
@@ -51,7 +51,7 @@
                 magma_analysis_dict[k]["fastqs_approved"] = False
 
     with open('magma_analysis.json', 'w') as f:
-        json.dump(magma_analysis_dict, f, indent=4)
+        json.dump(magma_analysis_dict, f, indent=4, ensure_ascii= False)
 
 # ============================================
 # Parse the validation reports for exact sample names which passed/failed

diff --git a/modules/fastq_utils/validator.nf b/modules/fastq_utils/validator.nf
@@ -12,10 +12,10 @@ process FASTQ_VALIDATOR {
         val ready
 
     output:
-        tuple val(meta), path("*.check.*csv")
+        tuple val(magmaName), path("*.check.*csv")
         path("*.check.*csv")                          , emit: check_result
         path("*.fastq_report.csv")                    , emit: fastq_report
-        tuple val(meta), path(sampleRead)             , emit: reads
+        tuple val(magmaName), path(sampleRead)        , emit: reads
 
     shell:
 
@@ -56,7 +56,7 @@ process FASTQ_VALIDATOR {
             VALIDATED=1
             STATUS="passed"
             echo -e "file,magma_name,fastq_utils_check" > !{sampleRead.simpleName}.check.${STATUS}.csv
-            echo -e "!{sampleRead},!{meta.id},${STATUS}" >> !{sampleRead.simpleName}.check.${STATUS}.csv
+            echo -e "!{sampleRead},!{magmaName},${STATUS}" >> !{sampleRead.simpleName}.check.${STATUS}.csv
 
             csvtk join -f file  !{sampleRead.simpleName}.fastq_statistics.csv !{sampleRead.simpleName}.check.${STATUS}.csv >  !{sampleRead.simpleName}.fastq_report.csv
 
@@ -69,7 +69,7 @@ process FASTQ_VALIDATOR {
             VALIDATED=0
             STATUS="failed"
             echo -e "file,magma_name,fastq_utils_check" > !{sampleRead.simpleName}.check.${STATUS}.csv
-            echo -e "!{sampleRead},!{meta.id},${STATUS}" >> !{sampleRead.simpleName}.check.${STATUS}.csv
+            echo -e "!{sampleRead},!{magmaName},${STATUS}" >> !{sampleRead.simpleName}.check.${STATUS}.csv
 
             csvtk join -f file  !{sampleRead.simpleName}.fastq_statistics.csv !{sampleRead.simpleName}.check.${STATUS}.csv  > !{sampleRead.simpleName}.fastq_report.csv
 

diff --git a/workflows/validate_fastqs_wf.nf b/workflows/validate_fastqs_wf.nf
@@ -35,11 +35,11 @@ workflow VALIDATE_FASTQS_WF {
                 //Accomodate single/multi reads
                 if (read1 && read2) {
 
-                    return [[id: magma_sample_name, paired: true, bam_rg_string:magma_bam_rg_string ], [file(read1, checkIfExists: true), file(read2, checkIfExists: true)]]
+                    return [ magma_sample_name,  [file(read1, checkIfExists: true), file(read2, checkIfExists: true)]]
 
                 } else {
 
-                    return [[id: magma_sample_name, paired: true, bam_rg_string:magma_bam_rg_string ],  [file(read1, checkIfExists: true)]]
+                    return [magma_sample_name, [file(read1, checkIfExists: true)]]
 
                     }
                 }