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Commit f1adf447 authored by Venkat Malladi's avatar Venkat Malladi
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Merge branch '35-fix-astrocyte' into 'master'

Move single-end to run on astrocyte.

Closes #35

See merge request !28
parents abeaa753 3cf06f92
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1 merge request!28Move single-end to run on astrocyte.
Pipeline #3590 canceled with stages
in 1 minute and 52 seconds
......@@ -32,7 +32,7 @@ single_end_mouse:
only:
- master
script:
- nextflow run workflow/main.nf --astrocyte 'false' -resume
- nextflow run workflow/main.nf --astrocyte 'true' -resume
- pytest -m singleend
artifacts:
expire_in: 2 days
......
......@@ -108,7 +108,7 @@ workflow_parameters:
end to the other, generating the sequence of base pairs. In paired-end
reading it starts at one read, finishes this direction at the specified
read length, and then starts another round of reading from the opposite
end of the fragment.
end of the fragment. (Paired-end: True, Single-end: False)
- id: design
type: file
......
......@@ -22,9 +22,9 @@ params.multiqc = "$baseDir/conf/multiqc_config.yaml"
if (params.astrocyte) {
print("Running under astrocyte")
referenceLocation = "/project/shared/bicf_workflow_ref"
params.bwaIndex = "$referenceLocation/$genome"
params.chromSizes = "$referenceLocation/$genome/genomefile.txt"
params.fasta = "$referenceLocation/$genome/genome.fa.txt"
params.bwaIndex = "$referenceLocation/$params.genome"
params.chromSizes = "$referenceLocation/$params.genome/genomefile.txt"
params.fasta = "$referenceLocation/$params.genome/genome.fa.txt"
if (params.genome == 'GRCh37' || params.genome == 'GRCh38') {
params.genomeSize = 'hs'
} else if (params.chromSizes == 'GRCm38') {
......
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