ngtax and picrust fixes

cwl/ngtax/ngtax.cwl

@@ -92,6 +92,8 @@ arguments:
   - prefix: "-fragment"
     valueFrom: $(inputs.fragment)
 
+stdout: ngtax2.stdout.log
+
 
 outputs:
   biom: 
@@ -102,6 +104,10 @@ outputs:
     type: File
     outputBinding:
       glob: "$(inputs.sample)_NG-Tax_$(inputs.for_read_len).ttl"
+  stdout_out:
+    type: File
+    outputBinding:
+      glob: ngtax2.stdout.log
 
 s:author:
   - class: s:Person

cwl/picrust2/picrust2_pipeline.cwl

@@ -8,9 +8,9 @@ doc: |
   Runs the PICRUSt2 pipeline workflow which is installed according to the following procedure:
 
   source /root/miniconda/bin/activate && \ 
-    cd /unlock/infrastructure/binaries/picrust2-2.4.1/ && \ 
-    conda env create -f /conda/picrust2_env.yml -p /unlock/infrastructure/conda/picrust2 && \ 
-    conda activate /unlock/infrastructure/conda/picrust2 && \ 
+    cd /unlock/infrastructure/conda/picrust2_v2.4.2 && \ 
+    conda env create -f /conda/picrust2_env.yml -p /unlock/infrastructure/conda/picrust2_v2.4.2 && \ 
+    conda activate /unlock/infrastructure/conda/picrust2_v2.4.2 && \ 
     pip install --editable . && \ 
 
   The folder can be obtained from the picrust2 repository.
@@ -24,8 +24,8 @@ requirements:
           #!/bin/bash
           source /root/miniconda/bin/activate
           conda init bash
-          conda activate /unlock/infrastructure/conda/picrust2
-          PATH="/unlock/infrastructure/conda/picrust2/bin/:$PATH"
+          conda activate /unlock/infrastructure/conda/picrust2_v2.4.2
+          PATH="/unlock/infrastructure/conda/picrust2_v2.4.2/bin/:$PATH"
           export PATH
           picrust2_pipeline.py $@
 
@@ -69,6 +69,9 @@ arguments:
   - prefix: "--in_traits"
     valueFrom: $(inputs.traits)
 
+stdout: $(inputs.identifier)_picrust2.stdout.log
+stderr: $(inputs.identifier)_picrust2.stderr.log
+
 outputs:
   EC_metagenome_out:
     type: Directory
@@ -122,6 +125,14 @@ outputs:
     type: File
     outputBinding:
       glob: $(inputs.identifier)_PICRUSt2/out.tre
+  stdout_out:
+    type: File
+    outputBinding:
+      glob: $(inputs.identifier)_picrust2.stdout.log
+  stderr_out:
+    type: File
+    outputBinding:
+      glob: $(inputs.identifier)_picrust2.stderr.log
  
 s:author:
   - class: s:Person

cwl/workflows/workflow_ngtax_picrust2.cwl

@@ -104,7 +104,7 @@ steps:
       sample: sample
       fragment: fragment
       primersRemoved: primersRemoved
-    out: [biom, turtle]
+    out: [biom, turtle, stdout_out]
 #############################
   ngtax_to_tsv-fasta:
     run: ../ngtax/ngtax_to_tsv-fasta.cwl
@@ -124,7 +124,7 @@ steps:
         input_table: ngtax_to_tsv-fasta/picrust_tsv
         fasta: ngtax_to_tsv-fasta/picrust_fasta
         threads: threads
-    out: [EC_metagenome_out,PFAM_metagenome_out,TIGRFAM_metagenome_out,COG_metagenome_out,KO_metagenome_out,intermediate,pathways_out,EC_predicted.tsv.gz,PFAM_predicted.tsv.gz,TIGRFAM_predicted.tsv.gz,KO_predicted.tsv.gz,marker_predicted_and_nsti.tsv.gz,out.tre]
+    out: [EC_metagenome_out,PFAM_metagenome_out,TIGRFAM_metagenome_out,COG_metagenome_out,KO_metagenome_out,intermediate,pathways_out,EC_predicted.tsv.gz,PFAM_predicted.tsv.gz,TIGRFAM_predicted.tsv.gz,KO_predicted.tsv.gz,marker_predicted_and_nsti.tsv.gz,out.tre,stdout_out,stderr_out]
 ############################
   folder_compression:
     when: $(inputs.fasta.size > 1024)
@@ -150,7 +150,7 @@ steps:
     run: ../expressions/files_to_folder.cwl
     in:
       files:
-        source: [ngtax/biom, ngtax/turtle]
+        source: [ngtax/biom, ngtax/turtle, ngtax/stdout_out]
       destination: 
         valueFrom: $("2_Classification")
     out:
@@ -161,7 +161,7 @@ steps:
     run: ../expressions/files_to_folder.cwl
     in:
       files:
-        source: [picrust2/EC_predicted.tsv.gz, picrust2/PFAM_predicted.tsv.gz, picrust2/TIGRFAM_predicted.tsv.gz, picrust2/KO_predicted.tsv.gz, picrust2/marker_predicted_and_nsti.tsv.gz, picrust2/out.tre, folder_compression/outfile]
+        source: [picrust2/EC_predicted.tsv.gz, picrust2/PFAM_predicted.tsv.gz, picrust2/TIGRFAM_predicted.tsv.gz, picrust2/KO_predicted.tsv.gz, picrust2/marker_predicted_and_nsti.tsv.gz, picrust2/out.tre, folder_compression/outfile, picrust2/stdout_out, picrust2/stderr_out]
         linkMerge: merge_flattened
       folders:
         source: [picrust2/EC_metagenome_out, picrust2/PFAM_metagenome_out, picrust2/TIGRFAM_metagenome_out, picrust2/COG_metagenome_out, picrust2/KO_metagenome_out, picrust2/pathways_out]