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fix: switch path to biowulf /data/CCBR_Pipeliner #104

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Merged
kelly-sovacool merged 2 commits into from
Jul 17, 2025
Merged

fix: switch path to biowulf /data/CCBR_Pipeliner #104

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521d381
fix: switch path to biowulf /data/CCBR_Pipeliner
kelly-sovacool Jul 17, 2025
584ed95
chore: update changelog
kelly-sovacool Jul 17, 2025
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4 changes: 3 additions & 1 deletion CHANGELOG.md
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@@ -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

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10 changes: 5 additions & 5 deletions README.md
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Expand Up @@ -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=<WORKDIR> -m/--runmode=<RUNMODE>
bash /data/CCBR_Pipeliner/Pipelines/ASPEN/.v1.0.6/aspen -w/--workdir=<WORKDIR> -m/--runmode=<RUNMODE>

Required Arguments:
1. WORKDIR : [Type: String]: Absolute or relative path to the output folder with write permissions.
Expand All @@ -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

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6 changes: 3 additions & 3 deletions aspen
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Expand Up @@ -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?
Expand Down Expand Up @@ -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
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2 changes: 1 addition & 1 deletion docs/deployment.md
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Expand Up @@ -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

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