From d94301cc0e8ad0ccabaa00a6ba3f2ee6acd4af21 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 31 May 2024 10:39:53 +0200 Subject: [PATCH 1/6] added sbatch to be excluded in sftp copy --- bu_isciii/conf/configuration.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/bu_isciii/conf/configuration.json b/bu_isciii/conf/configuration.json index a1b3a592..5b4601c9 100755 --- a/bu_isciii/conf/configuration.json +++ b/bu_isciii/conf/configuration.json @@ -16,7 +16,8 @@ "'.nextflow*'", "'*_DEL'", "'*.R'", - "'*.py'" + "'*.py'", + "'*.sbatch" ] }, "xtutatis_api_settings": { From 65e15eeea71a7870c79c16dcea5eb0215c018b7e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 31 May 2024 14:02:06 +0200 Subject: [PATCH 2/6] removed specific node from srun for exometrio template --- .../exometrio/ANALYSIS/ANALYSIS01_EXOME/03-annotation/lablog | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/03-annotation/lablog b/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/03-annotation/lablog index 2dd494ea..dfd600dd 100644 --- a/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/03-annotation/lablog +++ b/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 ${scratch_dir} --output logs/AWK.log --job-name AWK bash ./aux_03_awk.sh &" >> _03_Vep_plugin_dbNSFP_parse.sh From 536986211ff8054394076b2b4314aa4a01267c72 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 31 May 2024 14:12:35 +0200 Subject: [PATCH 3/6] removed save intermediate alignment files from rnaseq template --- .../templates/rnaseq/ANALYSIS/DATE_ANALYSIS01_RNASEQ/lablog | 1 - 1 file changed, 1 deletion(-) diff --git a/bu_isciii/templates/rnaseq/ANALYSIS/DATE_ANALYSIS01_RNASEQ/lablog b/bu_isciii/templates/rnaseq/ANALYSIS/DATE_ANALYSIS01_RNASEQ/lablog index 5060844f..d0674cda 100644 --- a/bu_isciii/templates/rnaseq/ANALYSIS/DATE_ANALYSIS01_RNASEQ/lablog +++ b/bu_isciii/templates/rnaseq/ANALYSIS/DATE_ANALYSIS01_RNASEQ/lablog @@ -24,7 +24,6 @@ export NXF_OPTS="-Xms500M -Xmx4G" -params-file ../../DOC/hg38_ensmbl_rnaseq.yml \\ --input samplesheet.csv \\ --outdir 01-$(date '+%Y%m%d')_rnaseq \\ - --save_align_intermeds \\ --skip_markduplicates \\ --pseudo_aligner salmon \\ -resume From 757fa3ebedcc40a5ffd9d40aeab53f95788e1eeb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 31 May 2024 14:19:26 +0200 Subject: [PATCH 4/6] updated changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1801c592..0ee8f4a9 100755 --- a/CHANGELOG.md +++ b/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 From e3bc82cd1809c3c2726876e7c30e64716038b406 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 31 May 2024 14:24:23 +0200 Subject: [PATCH 5/6] fix try for github action for python linting --- .github/workflows/python_lint.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/python_lint.yml b/.github/workflows/python_lint.yml index 9d043bbd..1b180299 100644 --- a/.github/workflows/python_lint.yml +++ b/.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: From cda373d4592697ca8e30bb672e9b9bbcba5f22ce Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 31 May 2024 14:35:08 +0200 Subject: [PATCH 6/6] Minor version fix in github action file --- .github/workflows/python_lint.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python_lint.yml b/.github/workflows/python_lint.yml index 1b180299..d121b7f3 100644 --- a/.github/workflows/python_lint.yml +++ b/.github/workflows/python_lint.yml @@ -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