diff --git a/ngs_pipeline.snakefile b/ngs_pipeline.snakefile index eb66e7d..ca19c3f 100644 --- a/ngs_pipeline.snakefile +++ b/ngs_pipeline.snakefile @@ -298,10 +298,11 @@ for subject in SUBJECT_VCFS.keys(): ALL_VCFs +=[vcf] ########################################################################### onerror: - shell("find .snakemake/ -group $USER -exec chgrp -f {GROUP} {{}} \;") + shell("find . -group $USER -exec chgrp -f {GROUP} {{}} \;") shell("find . \( -type f -user $USER -exec chmod g+rw {{}} \; \) , \( -type d -user $USER -exec chmod g+rwx {{}} \; \)") shell("ssh {HOST} \"echo 'Pipeline failed on {PATIENTS}. Error occured on {HOST}. Working Dir: {WORK_DIR}' |mutt -s 'Khanlab ngs-pipeline Status' `whoami`@mail.nih.gov {MAIL} \"") + shell("find .snakemake/ -group $USER -exec chgrp -f {GROUP} {{}} \;") onstart: shell("ssh {HOST} \"echo 'ngs-pipeline started on {PATIENTS} on {HOST}. Working Dir: {WORK_DIR}' |mutt -s 'Khanlab ngs-pipeline Status' `whoami`@mail.nih.gov {MAIL} \"") onsuccess: @@ -340,7 +341,6 @@ rule Khanlab_Pipeline: do touch {WORK_DIR}/${{sub}}/{TIME}/successful.txt done - find log/ -type f -empty -delete find . -group $USER -exec chgrp -f {params.group} {{}} \; find . \( -type f -user $USER -exec chmod g+rw {{}} \; \) , \( -type d -user $USER -exec chmod g+rwx {{}} \; \) export LC_ALL=C