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Merged
rernst merged 6 commits into from
Jun 9, 2023
Merged

Release/v0.7.1 #72

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a632db8
Add sylabs uri
rernst Dec 16, 2022
ee9605d
Add sylabs uri
rernst Dec 16, 2022
bc410d1
Merge branch 'develop' into feature/hpc_rocky
rernst May 16, 2023
c4f7982
Merge branch 'develop' into feature/hpc_rocky
rernst May 31, 2023
e6b9740
Merge pull request #71 from UMCUGenetics/feature/hpc_rocky
rernst Jun 8, 2023
fcd72d7
Merge branch 'develop' into release/v0.7.1
rernst Jun 8, 2023
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2 changes: 1 addition & 1 deletion BWA-Mapping/bwa-0.7.17_samtools-1.9/Mapping.nf
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Expand Up @@ -2,7 +2,7 @@ process BWAMapping {
tag {"BWA Mem ${sample_id} - ${rg_id}"}
label 'BWA_0_7_17'
label 'BWA_0_7_17_Mem'
container = 'library://sawibo/default/bioinf-tools:bwa-0.7.17_samtools-1.9'
container = 'library://library.sylabs.io/sawibo/default/bioinf-tools:bwa-0.7.17_samtools-1.9'
shell = ['/bin/bash', '-euo', 'pipefail']

input:
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2 changes: 1 addition & 1 deletion ControlFREEC/11.5/AssessSignificance.nf
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Expand Up @@ -2,7 +2,7 @@ process AssessSignificance {
tag {"Control Freec AssessSignificance ${sample_id}"}
label 'ControlFreec_11_5'
label 'ControlFreec_11_5_AssessSignificance'
container = 'library://sawibo/default/bioinf-tools:freec11.5'
container = 'library://library.sylabs.io/sawibo/default/bioinf-tools:freec11.5'
shell = ['/bin/bash', '-euo', 'pipefail']

input:
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3 changes: 1 addition & 2 deletions ControlFREEC/11.5/Freec.nf
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Expand Up @@ -2,8 +2,7 @@ process Freec {
tag {"Control Freec ${sample_id}"}
label 'ControlFreec_11_5'
label 'ControlFreec_11_5_Freec'
//TODO: upload to singularity library
container = 'library://sawibo/default/bioinf-tools:freec11.5'
container = 'library://library.sylabs.io/sawibo/default/bioinf-tools:freec11.5'
shell = ['/bin/bash', '-euo', 'pipefail']

input:
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2 changes: 1 addition & 1 deletion ControlFREEC/11.5/MakeGraph.nf
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Expand Up @@ -2,7 +2,7 @@ process MakeGraph {
tag {"Control Freec MakeGraph ${sample_id}"}
label 'ControlFreec_11_5'
label 'ControlFreec_11_5_MakeGraph'
container = 'library://sawibo/default/bioinf-tools:freec11.5'
container = 'library://library.sylabs.io/sawibo/default/bioinf-tools:freec11.5'
shell = ['/bin/bash', '-euo', 'pipefail']

input:
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2 changes: 1 addition & 1 deletion ControlFREEC/11.5/MakeKaryotype.nf
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Expand Up @@ -2,7 +2,7 @@ process MakeKaryotype {
tag {"Control Freec MakeKaryotype ${sample_id}"}
label 'ControlFreec_11_5'
label 'ControlFreec_11_5_MakeKaryotype'
container = 'library://sawibo/default/bioinf-tools:freec11.5'
container = 'library://library.sylabs.io/sawibo/default/bioinf-tools:freec11.5'
shell = ['/bin/bash', '-euo', 'pipefail']

input:
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