Merge pull request #1 from jerdra/develop

catch up to develop and tigrlab
TIGRLab · Jul 8, 2019 · 1ae7182 · 1ae7182
2 parents a323ee3 + b18e315
commit 1ae7182
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Showing 6 changed files with 16 additions and 9 deletions.
diff --git a/bids.nf b/bids.nf
@@ -114,11 +114,21 @@ process run_bids{
     file sub_input from invoke_json
 
     output:
-    file '.command.log' 
+    file '.command.*' into logs
 
     beforeScript "source /etc/profile"
     scratch true
-    publishDir "$params.out/logs", mode: 'move', saveAs: {"$sub_input".replace('.json','.log') }
+
+    publishDir "$params.out/pipeline_logs", \
+                 mode: 'copy', \
+                 saveAs: { "$sub_input".replace('.json','.out')}, \
+                 pattern: '.command.out'
+
+    publishDir "$params.out/pipeline_logs", \
+                 mode: 'copy', \
+                 saveAs: { "$sub_input".replace('.json','.err')}, \
+                 pattern: '.command.err'
+
     module 'slurm'
 
     shell:
@@ -142,5 +152,3 @@ process run_bids{
 
     '''
 }
-
-// stdout into a log file
diff --git a/nextflow_config/fmriprep-1.3.2.nf.config b/nextflow_config/fmriprep-1.3.2.nf.config
@@ -63,8 +63,8 @@ params.application = "FMRIPREP"
 process {
     withName: run_bids {
 
-        errorStrategy = "retry"
         maxErrors = 3
+        errorStrategy = {task.attempt == task.maxErrors ? "retry" : "ignore"}
         clusterOptions = "--time=24:00:00 --mem-per-cpu=4096\
          --cpus-per-task=4 --job-name fmriprep_pipeline\
          --nodes=1"

diff --git a/nextflow_config/fmriprep_ciftify-1.3.0-post2-2.3.1.nf.config b/nextflow_config/fmriprep_ciftify-1.3.0-post2-2.3.1.nf.config
@@ -63,8 +63,8 @@ params.application = "FMRIPREP_CIFTIFY"
 process {
     withName: run_bids {
 
-        errorStrategy = "retry"
         maxErrors = 3
+        errorStrategy = {task.attempt == task.maxErrors ? "retry" : "ignore"}
         clusterOptions = "--time=24:00:00 --mem-per-cpu=1024 \
          --cpus-per-task=4 --job-name ciftify_pipeline \
          --nodes=1"

diff --git a/nextflow_config/freesurfer-6.0.1.nf.config b/nextflow_config/freesurfer-6.0.1.nf.config
@@ -63,8 +63,8 @@ params.application = "FREESURFER"
 process {
     withName: run_bids {
 
-        errorStrategy = "retry"
         maxErrors = 3
+        errorStrategy = {task.attempt == task.maxErrors ? "retry" : "ignore"}
         clusterOptions = "--time=24:00:00 --mem-per-cpu=2048\
          --cpus-per-task=2 --job-name freesurfer_pipeline\
          --nodes=1"

diff --git a/nextflow_config/mriqc-0.14.2.nf.config b/nextflow_config/mriqc-0.14.2.nf.config
@@ -64,8 +64,8 @@ process {
     withName: run_bids {
 
 
-        errorStrategy = "retry"
         maxErrors = 3
+        errorStrategy = {task.attempt == task.maxErrors ? "retry" : "ignore"}
         clusterOptions = "--time=4:00:00 --mem-per-cpu=2048\
          --cpus-per-task=4 --job-name mriqc_pipeline\
          --nodes=1"

diff --git a/requirements.txt b/requirements.txt
@@ -6,7 +6,6 @@ idna==2.6
 jsonschema==2.6.0
 mock==3.0.5
 more-itertools==7.0.0
-pkg-resources==0.0.0
 pluggy==0.6.0
 py==1.8.0
 pytest==3.5.0