merge with sfitz-by-readgroup complete and tested

Author: sorelfitzgibbon

main.nf

@@ -162,9 +162,9 @@ workflow {
             samples_to_process_ch
             )
         }
-    if ('fastqc' in params.algorithms) {
+    if ('fastqc' in params.algorithm) {
         assess_ReadQuality_FastQC(
-            samplesToProcessChannel
+            samples_to_process_ch
             )
         }
     if ('collectwgsmetrics' in params.algorithm) {

module/fastqc.nf

@@ -14,18 +14,18 @@ process assess_ReadQuality_FastQC {
         pattern: "${output_filename}",
         mode: "copy",
         enabled: true
-    ext log_dir_suffix: { "-${id}" }
+    ext log_dir_suffix: { "-${sm_id}" }
 
     input:
-        tuple val(orig_id), val(id), path(path), val(read_length), val(sample_type)
+        tuple path(path), val(unused), val(sm_id), val(rg_arg), val(unused), val(unused), val(unused), val(read_length)
 
     output:
         path("${output_filename}")
 
     script:
     output_filename = generate_standard_filename("FastQC-${params.fastqc_version}",
         params.dataset_id,
-        id,
+        sm_id,
         [:])
 
     """

test/config/fastqc.config

@@ -8,7 +8,7 @@ includeConfig "${projectDir}/nextflow.config"
 
 // Inputs/parameters of the pipeline
 params {
-    algorithms = ['fastqc']
+    algorithm = ['fastqc']
     reference = '/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
     blcds_registered_dataset = false // if you want the output to be registered
     save_intermediate_files = true