Commit 49710b22 authored by Jasper Koehorst's avatar Jasper Koehorst
Browse files

ngtax and picrust fixes

parent d944d61d
......@@ -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_$(inputs.for_read_len).ttl"
stdout_out:
type: File
outputBinding:
glob: ngtax2.stdout.log
s:author:
- class: s:Person
......
......@@ -8,9 +8,9 @@ doc: |
Runs the PICRUSt2 pipeline workflow which is installed according to the following procedure:
source /root/miniconda/bin/activate && \
cd /unlock/infrastructure/binaries/picrust2-2.4.1/ && \
conda env create -f /conda/picrust2_env.yml -p /unlock/infrastructure/conda/picrust2 && \
conda activate /unlock/infrastructure/conda/picrust2 && \
cd /unlock/infrastructure/conda/picrust2_v2.4.2 && \
conda env create -f /conda/picrust2_env.yml -p /unlock/infrastructure/conda/picrust2_v2.4.2 && \
conda activate /unlock/infrastructure/conda/picrust2_v2.4.2 && \
pip install --editable . && \
The folder can be obtained from the picrust2 repository.
......@@ -24,8 +24,8 @@ requirements:
#!/bin/bash
source /root/miniconda/bin/activate
conda init bash
conda activate /unlock/infrastructure/conda/picrust2
PATH="/unlock/infrastructure/conda/picrust2/bin/:$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
......
......@@ -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]
......
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