diff --git a/CHANGELOG.md b/CHANGELOG.md index b45c4c5..602f9f0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,10 +1,12 @@ ## ASPEN development version +- Fix broken data path for biowulf. (#104, @kelly-sovacool) + ## ASPEN 1.1.1 - Fix Diffatac error (#101, @kopardev) - Adds a defensive check to prevent invalid 'row.names' length error when up_roi or down_roi are empty (due to strict FC/FDR thresholds in DiffATAC) -- Minor refactoring to accomodate moving to ccbr_tools >= v0.4 (#101, @kopardev) +- Minor refactoring to accommodate moving to ccbr_tools >= v0.4 (#101, @kopardev) ## ASPEN 1.1.0 diff --git a/README.md b/README.md index ab73a15..ca3d5aa 100644 --- a/README.md +++ b/README.md @@ -47,7 +47,7 @@ aspen calls peaks using the following tools: * Genrich [RECOMMENDED FOR USE] USAGE: - bash /gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/ASPEN/.v1.0.6/aspen -w/--workdir= -m/--runmode= + bash /data/CCBR_Pipeliner/Pipelines/ASPEN/.v1.0.6/aspen -w/--workdir= -m/--runmode= Required Arguments: 1. WORKDIR : [Type: String]: Absolute or relative path to the output folder with write permissions. @@ -71,16 +71,16 @@ Optional Arguments: --help|-h : print this help Example commands: - bash /gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/ASPEN/.v1.0.6/aspen -w=/my/output/folder -m=init - bash /gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/ASPEN/.v1.0.6/aspen -w=/my/output/folder -m=dryrun - bash /gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/ASPEN/.v1.0.6/aspen -w=/my/output/folder -m=run + bash /data/CCBR_Pipeliner/Pipelines/ASPEN/.v1.0.6/aspen -w=/my/output/folder -m=init + bash /data/CCBR_Pipeliner/Pipelines/ASPEN/.v1.0.6/aspen -w=/my/output/folder -m=dryrun + bash /data/CCBR_Pipeliner/Pipelines/ASPEN/.v1.0.6/aspen -w=/my/output/folder -m=run ########################################################################################## VersionInfo: python : python/3.10 snakemake : snakemake - pipeline_home : /gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/ASPEN/.v1.0.6 + pipeline_home : /data/CCBR_Pipeliner/Pipelines/ASPEN/.v1.0.6 git commit/tag : f4366158ad972bc667422dcd4783bd69fa041556 v1.0.6 aspen_version : v1.0.6 diff --git a/aspen b/aspen index 0d063f8..f10c54e 100755 --- a/aspen +++ b/aspen @@ -308,8 +308,8 @@ function set_singularity_binds(){ echo "$PIPELINE_HOME" > ${WORKDIR}/tmp1 echo "$WORKDIR" >> ${WORKDIR}/tmp1 grep -o '\/.*' <(cat ${WORKDIR}/config.yaml ${WORKDIR}/samples.tsv) | tr '\t' '\n' | grep -v ' \|\/\/' | sort | uniq >> ${WORKDIR}/tmp1 - grep "^/" ${WORKDIR}/tmp1 | grep gpfs | awk -F'/' -v OFS='/' '{print $1,$2,$3,$4,$5}' | sort | uniq > ${WORKDIR}/tmp2 - grep "^/" ${WORKDIR}/tmp1 | grep -v gpfs | awk -F'/' -v OFS='/' '{print $1,$2,$3}' | sort | uniq > ${WORKDIR}/tmp3 + grep "^/" ${WORKDIR}/tmp1 | grep /vf | awk -F'/' -v OFS='/' '{print $1,$2,$3,$4,$5}' | sort | uniq > ${WORKDIR}/tmp2 + grep "^/" ${WORKDIR}/tmp1 | grep -v /vf | awk -F'/' -v OFS='/' '{print $1,$2,$3}' | sort | uniq > ${WORKDIR}/tmp3 while read a;do readlink -f $a;done < ${WORKDIR}/tmp3 > ${WORKDIR}/tmp4 binds=$(cat ${WORKDIR}/tmp2 ${WORKDIR}/tmp3 ${WORKDIR}/tmp4 | sort | uniq | tr '\n' ',') rm -f ${WORKDIR}/tmp? @@ -581,7 +581,7 @@ fi cat > ${WORKDIR}/submit_script.sbatch << EOF #!/bin/bash -#SBATCH --job-name="apsen" +#SBATCH --job-name="aspen" #SBATCH --mem=40g #SBATCH --partition=$PARTITIONS #SBATCH --time=96:00:00 diff --git a/docs/deployment.md b/docs/deployment.md index 339501e..2f5cf2e 100644 --- a/docs/deployment.md +++ b/docs/deployment.md @@ -120,7 +120,7 @@ Example commands: VersionInfo: python : python/3.10 snakemake : snakemake - pipeline_home : /gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/ASPEN/feature_spikeins + pipeline_home : /data/CCBR_Pipeliner/Pipelines/ASPEN/feature_spikeins git commit/tag : fc0699d6a7f9766963c8e7020c01214966616fab v1.0.6-29-gfc0699d aspen_version : v1.0.6-dev-spikeins