Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Fix cache names #260

Merged
merged 3 commits into from
Mar 4, 2024
Merged

Fix cache names #260

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
7ec6ca4
Update plink2_makebed.nf
smlmbrt Mar 2, 2024
1987458
Fix prefix and output names
smlmbrt Mar 2, 2024
80d87b3
Remove chromosome ID from orient
smlmbrt Mar 2, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion modules/local/ancestry/oadp/fraposa_pca.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ process FRAPOSA_PCA {
path "versions.yml", emit: versions

script:
output = "${params.target_build}_${meta.id}_${meta.chrom}"
output = "${params.target_build}_${meta.id}"
"""
fraposa ${ref_geno.baseName} \
--method $params.projection_method \
Expand Down
6 changes: 3 additions & 3 deletions modules/local/ancestry/oadp/plink2_makebed.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ process PLINK2_MAKEBED {
label "${ params.copy_genomes ? 'copy_genomes' : '' }"
label "plink2" // controls conda, docker, + singularity options

tag "$meta.id chromosome"
tag "$meta.id"

storeDir workDir / "ancestry" / "bed"

Expand Down Expand Up @@ -33,8 +33,8 @@ process PLINK2_MAKEBED {
// output options
def extract = pruned.name != 'NO_FILE' ? "--extract $pruned" : ''
def extracted = pruned.name != 'NO_FILE' ? "_extracted" : ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}_" : "${meta.id}_"
output = "${params.target_build}_${prefix}${meta.chrom}${extracted}"
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
output = "${params.target_build}_${prefix}${extracted}"
split_output = "${meta.id}_splitfam"
"""
# use explicit flag because pfile prefix might be different
Expand Down
4 changes: 2 additions & 2 deletions modules/local/ancestry/oadp/plink2_orient.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -30,8 +30,8 @@ process PLINK2_ORIENT {
def mem_mb = task.memory.toMega() // plink is greedy

// output options
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}_" : "${meta.id}_"
output = "${params.target_build}_${prefix}${meta.chrom}_oriented"
def prefix = task.ext.suffix ? "_${meta.id}${task.ext.suffix}" : "_${meta.id}"
output = "${params.target_build}${prefix}_oriented"
"""
plink2 \
--threads $task.cpus \
Expand Down
Loading