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Commit 3cf06f92 authored by Venkat Malladi's avatar Venkat Malladi
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Move single-end to run on astrocyte.

parent abeaa753
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......@@ -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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