Template issues

.github/workflows/python_lint.yml

@@ -3,10 +3,10 @@ name: python_lint
 on:
   push:
     paths:
-      - '**.py'
+      - '**/*.py'
   pull_request:
     paths:
-      - '**.py'
+      - '**/*.py'
 
 jobs:
   flake8_py3:
@@ -18,7 +18,7 @@ jobs:
           python-version: 3.9.x
           architecture: x64
       - name: Checkout PyTorch
-        uses: actions/checkout@master
+        uses: actions/checkout@v2
       - name: Install flake8
         run: pip install flake8
       - name: Run flake8

CHANGELOG.md

@@ -39,6 +39,7 @@ Code contributions to the new version:
 - Added "01" to results folder creation in assembly template.
 - Some prompt answers limited to 1 character in lablog_viralrecon.
 - Created lablog_mtbseq_results. [#270](https://github.com/BU-ISCIII/buisciii-tools/pull/270)
+- PR #271. Closes [#235](https://github.com/BU-ISCIII/buisciii-tools/issues/235), [#228](https://github.com/BU-ISCIII/buisciii-tools/issues/228) and [#196](https://github.com/BU-ISCIII/buisciii-tools/issues/196)
 
 ### Modules
 

bu_isciii/conf/configuration.json

@@ -16,7 +16,8 @@
             "'.nextflow*'",
             "'*_DEL'",
             "'*.R'",
-            "'*.py'"
+            "'*.py'",
+            "'*.sbatch"
         ]
     },
     "xtutatis_api_settings": {

bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/03-annotation/lablog

@@ -42,7 +42,7 @@ echo "sed -i 's/#Uploaded_variation/ID/' ./vep/vep_annot_head.txt" >> _03_Vep_pl
 # Merge vep_plugin.txt with dbNSFP_ENSG_gene_GRCh37.txt by "Gene" column, save as vep_dbNSFP.txt. 
 # Merge vep_dbNSFP.txt with variants.table by "ID" column, save as variants_annot_all.tab
 
-echo "srun --partition short_idx --nodelist ideafix04 --mem 200G --time 12:00:00 --chdir ${scratch_dir} --output logs/MERGE_ALL.log --job-name MERGE_ALL Rscript Merge_All.R" >> _03_Vep_plugin_dbNSFP_parse.sh
+echo "srun --partition short_idx --mem 200G --time 12:00:00 --chdir ${scratch_dir} --output logs/MERGE_ALL.log --job-name MERGE_ALL Rscript Merge_All.R" >> _03_Vep_plugin_dbNSFP_parse.sh
 
 echo "srun --partition short_idx --time 2:00:00 --chdir ${scratch_dir} --output logs/AWK.log --job-name AWK bash ./aux_03_awk.sh &" >> _03_Vep_plugin_dbNSFP_parse.sh
 

bu_isciii/templates/rnaseq/ANALYSIS/DATE_ANALYSIS01_RNASEQ/lablog

@@ -24,7 +24,6 @@ export NXF_OPTS="-Xms500M -Xmx4G"
           -params-file ../../DOC/hg38_ensmbl_rnaseq.yml \\
           --input samplesheet.csv \\
           --outdir 01-$(date '+%Y%m%d')_rnaseq \\
-          --save_align_intermeds \\
           --skip_markduplicates \\
           --pseudo_aligner salmon \\
           -resume