diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml index a8ff755..47172f1 100644 --- a/.github/release-drafter.yml +++ b/.github/release-drafter.yml @@ -1,5 +1,5 @@ -name-template: 'v$NEXT_PATCH_VERSION' -tag-template: 'v$NEXT_PATCH_VERSION' +name-template: 'v$NEXT_MINOR_VERSION' +tag-template: 'v$NEXT_MINOR_VERSION' categories: - title: '🧬 Features' labels: @@ -31,4 +31,4 @@ template: | ## Changes $CHANGES ## 🕵️‍♀️ Full commit logs - - https://github.com/oncokb/oncokb-annotator/compare/$PREVIOUS_TAG...v$NEXT_PATCH_VERSION + - https://github.com/oncokb/oncokb-annotator/compare/$PREVIOUS_TAG...v$NEXT_MINOR_VERSION diff --git a/.github/workflows/compare-study-annotation.yml b/.github/workflows/compare-study-annotation.yml index 4758fae..3b11af0 100644 --- a/.github/workflows/compare-study-annotation.yml +++ b/.github/workflows/compare-study-annotation.yml @@ -36,40 +36,40 @@ jobs: git checkout -b compare STUDY=msk_impact_2017 - DATAHUB_URL=https://media.githubusercontent.com/media/cBioPortal/datahub/42afc279efb8d9104aba36fa35bad3ec41921949/public/$STUDY + DATAHUB_URL=https://media.githubusercontent.com/media/cBioPortal/datahub/42afc279efb8d9104aba36fa35bad3ec41921949/public/"$STUDY" MUTATION_DATA_NAME=data_mutations_extended.txt CLINICAL_DATA_NAME=data_clinical_sample.txt FUSION_DATA_NAME=data_fusions.txt CNA_DATA_NAME=data_CNA.txt - cd data - curl -s $DATAHUB_URL/$MUTATION_DATA_NAME -O - curl -s $DATAHUB_URL/$CLINICAL_DATA_NAME -O - curl -s $DATAHUB_URL/$FUSION_DATA_NAME -O - curl -s $DATAHUB_URL/$CNA_DATA_NAME -O + cd data || exit + curl -s "$DATAHUB_URL"/"$MUTATION_DATA_NAME" -O + curl -s "$DATAHUB_URL"/"$CLINICAL_DATA_NAME" -O + curl -s "$DATAHUB_URL"/"$FUSION_DATA_NAME" -O + curl -s "$DATAHUB_URL"/"$CNA_DATA_NAME" -O cd .. # create compare folder to add all annotated files mkdir compare PREFIX=oncokb - IMAF=data/$MUTATION_DATA_NAME - OMAF=compare/"$PREFIX"_$MUTATION_DATA_NAME + IMAF=data/"$MUTATION_DATA_NAME" + OMAF=compare/"$PREFIX"_"$MUTATION_DATA_NAME" - IC=data/$CLINICAL_DATA_NAME - OC=compare/"$PREFIX"_$CLINICAL_DATA_NAME + IC=data/"$CLINICAL_DATA_NAME" + OC=compare/"$PREFIX"_"$CLINICAL_DATA_NAME" - IF=data/$FUSION_DATA_NAME - OF=compare/"$PREFIX"_$FUSION_DATA_NAME + IF=data/"$FUSION_DATA_NAME" + OF=compare/"$PREFIX"_"$FUSION_DATA_NAME" - ICNA=data/$CNA_DATA_NAME - OCNA=compare/"$PREFIX"_$CNA_DATA_NAME + ICNA=data/"$CNA_DATA_NAME" + OCNA=compare/"$PREFIX"_"$CNA_DATA_NAME" - python MafAnnotator.py -i $IMAF -o $OMAF -c $IC -b $ONCOKB_API_TOKEN - python FusionAnnotator.py -i $IF -o $OF -c $IC -b $ONCOKB_API_TOKEN - python CnaAnnotator.py -i $ICNA -o $OCNA -c $IC -b $ONCOKB_API_TOKEN - python ClinicalDataAnnotator.py -i $IC -o $OC -a $OMAF,$OCNA,$OF + python MafAnnotator.py -i "$IMAF" -o "$OMAF" -c "$IC" -b "$ONCOKB_API_TOKEN" + python FusionAnnotator.py -i "$IF" -o "$OF" -c "$IC" -b "$ONCOKB_API_TOKEN" + python CnaAnnotator.py -i "$ICNA" -o "$OCNA" -c "$IC" -b "$ONCOKB_API_TOKEN" + python ClinicalDataAnnotator.py -i "$IC" -o "$OC" -a "$OMAF,$OCNA,$OF" git config user.name oncokb-bot git config user.email dev.oncokb@gmail.com @@ -89,7 +89,7 @@ jobs: # remove everything under compare folder and replace wiht the ones from oncokb-data rm -f compare/*.txt - cd compare + cd compare || exit curl -s -H "Authorization: token ${ONCOKB_OAUTH_TOKEN}" https://api.github.com/repos/knowledgesystems/oncokb-data/contents/annotation/$STUDY | jq -r '.[] | .download_url + " " + .name' | while IFS=' ' read -r downloadurl name; do if [[ "$name" == "$FIEL_NAME_PREFIX"* ]]; then curl -s "$downloadurl" -o $name diff --git a/example.sh b/example.sh index 2da5b9c..fa9379e 100644 --- a/example.sh +++ b/example.sh @@ -1,36 +1,44 @@ #!/usr/bin/env bash IMAF="data/example_maf.txt" OMAF="data/example_maf.oncokb.txt" + IMAF38="data/example_maf_grch38.txt" OMAF38="data/example_maf_grch38.oncokb.txt" + OMAFHGVSPSHORT="data/example_maf_hgsp_short.oncokb.txt" OMAFHGVSP="data/example_maf_hgsp.oncokb.txt" OMAFHGVSG="data/example_maf_hgsg.oncokb.txt" OMAFGC="data/example_maf_genomic_change.oncokb.txt" + IATYPICALALT="data/example_atypical_alterations.txt" OATYPICALALT="data/example_atypical_alterations.oncokb.txt" + IF="data/example_fusions.txt" OF="data/example_fusions.oncokb.txt" + ICNA="data/example_cna.txt" OCNA="data/example_cna.oncokb.txt" + IC="data/example_clinical.txt" OC="data/example_clinical.oncokb.txt" + OCPDF="data/example_clinical.oncokb.pdf" + TOKEN="" #OncoKB API Token README="data/example_README.txt" -python MafAnnotator.py -i $IMAF -o $OMAF -c $IC -b $TOKEN -python MafAnnotator.py -i $IMAF -o $OMAFHGVSPSHORT -c $IC -b $TOKEN -q hgvsp_short -python MafAnnotator.py -i $IMAF -o $OMAFHGVSP -c $IC -b $TOKEN -q hgvsp -python MafAnnotator.py -i $IMAF -o $OMAFHGVSG -c $IC -b $TOKEN -q hgvsg -python MafAnnotator.py -i $IMAF -o $OMAFGC -c $IC -b $TOKEN -q genomic_change +python MafAnnotator.py -i "$IMAF" -o "$OMAF" -c "$IC" -b "$TOKEN" +python MafAnnotator.py -i "$IMAF" -o "$OMAFHGVSPSHORT" -c "$IC" -b "$TOKEN" -q hgvsp_short +python MafAnnotator.py -i "$IMAF" -o "$OMAFHGVSP" -c "$IC" -b "$TOKEN" -q hgvsp +python MafAnnotator.py -i "$IMAF" -o "$OMAFHGVSG" -c "$IC" -b "$TOKEN" -q hgvsg +python MafAnnotator.py -i "$IMAF" -o "$OMAFGC" -c "$IC" -b "$TOKEN" -q genomic_change -python MafAnnotator.py -i $IMAF38 -o $OMAF38 -c $IC -b $TOKEN +python MafAnnotator.py -i "$IMAF38" -o "$OMAF38" -c "$IC" -b "$TOKEN" -python MafAnnotator.py -i $IATYPICALALT -o $OATYPICALALT -c $IC -b $TOKEN +python MafAnnotator.py -i "$IATYPICALALT" -o "$OATYPICALALT" -c "$IC" -b "$TOKEN" -python FusionAnnotator.py -i $IF -o $OF -c $IC -b $TOKEN -python CnaAnnotator.py -i $ICNA -o $OCNA -c $IC -b $TOKEN -python ClinicalDataAnnotator.py -i $IC -o $OC -a $OMAF,$OATYPICALALT,$OCNA,$OF -python OncoKBPlots.py -i $OC -o $OCPDF -c ONCOTREE_CODE #-n 10 -python GenerateReadMe.py -o $README +python FusionAnnotator.py -i "$IF" -o "$OF" -c "$IC" -b "$TOKEN" +python CnaAnnotator.py -i "$ICNA" -o "$OCNA" -c "$IC" -b "$TOKEN" +python ClinicalDataAnnotator.py -i "$IC" -o "$OC" -a "$OMAF,$OATYPICALALT,$OCNA,$OF" +python OncoKBPlots.py -i "$OC" -o "$OCPDF" -c ONCOTREE_CODE #-n 10 +python GenerateReadMe.py -o "$README"