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change to epytope 3.3.1 version and new multi container for peptide prediction #200

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change to epytope 3.3.1 version and new multi container for peptide prediction #200

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5856069
test with lower transcript number
jonasscheid Aug 3, 2022
47d1120
Merge branch 'nf-core:dev' into dev
jonasscheid Aug 31, 2022
340efa5
Merge branch 'nf-core:dev' into dev
jonasscheid Sep 3, 2022
9cb7b25
Merge branch 'nf-core:dev' into dev
jonasscheid Nov 19, 2022
6c0d3c5
Merge branch 'nf-core:dev' into dev
jonasscheid Dec 7, 2022
ca83f9e
Merge branch 'nf-core:dev' into dev
jonasscheid Dec 17, 2022
1db12d2
Merge branch 'nf-core:dev' into dev
jonasscheid Jan 25, 2023
80e7731
Merge branch 'nf-core:dev' into dev
jonasscheid May 3, 2023
5f5eec8
Adjust to new epytope 3.3.0 release and new multicontainer
jonasscheid May 3, 2023
682b69c
Testing new multicontainer -> fails somehow with import vcf
jonasscheid May 31, 2023
c8bbf94
new container
jonasscheid Jul 26, 2023
1298cfb
update epytope version
jonasscheid Jul 26, 2023
fa3780c
Merge branch 'dev' into dev
jonasscheid Jul 26, 2023
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6 changes: 3 additions & 3 deletions modules/local/epytope_check_requested_models.nf
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Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
process EPYTOPE_CHECK_REQUESTED_MODELS {
label 'process_low'

conda "bioconda::epytope=3.1.0"
conda "bioconda::epytope=3.3.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/epytope:3.1.0--pyh5e36f6f_0' :
'biocontainers/epytope:3.1.0--pyh5e36f6f_0' }"
'https://depot.galaxyproject.org/singularity/epytope:3.3.1--pyh7cba7a3_0' :
'biocontainers/epytope:3.3.1--pyh7cba7a3_0' }"

input:
tuple val(meta), path(input_file)
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6 changes: 3 additions & 3 deletions modules/local/epytope_generate_peptides.nf
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Expand Up @@ -2,10 +2,10 @@ process EPYTOPE_GENERATE_PEPTIDES {
label 'process_low'
tag "${meta.sample}"

conda "bioconda::epytope=3.1.0"
conda "bioconda::epytope=3.3.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/epytope:3.1.0--pyh5e36f6f_0' :
'biocontainers/epytope:3.1.0--pyh5e36f6f_0' }"
'https://depot.galaxyproject.org/singularity/epytope:3.3.1--pyh7cba7a3_0' :
'biocontainers/epytope:3.3.1--pyh7cba7a3_0' }"

input:
tuple val(meta), path(raw)
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4 changes: 1 addition & 3 deletions modules/local/epytope_peptide_prediction.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -2,9 +2,7 @@ process EPYTOPE_PEPTIDE_PREDICTION {
label 'process_low'

conda "conda-forge::coreutils=9.1 conda-forge::tcsh=6.20.00 bioconda::epytope=3.1.0 conda-forge::gawk=5.1.0 conda-forge::perl=5.32.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-11bbf0d242ea96f7b9c08d5b5bc26f2cd5ac5943:3419f320edefe6077631798f50d7bd4f8dc4763f-0' :
'biocontainers/mulled-v2-11bbf0d242ea96f7b9c08d5b5bc26f2cd5ac5943:3419f320edefe6077631798f50d7bd4f8dc4763f-0' }"
container 'ghcr.io/jonasscheid/epitopeprediction-2:0.3.0'

input:
tuple val(meta), path(splitted), path(software_versions)
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8 changes: 4 additions & 4 deletions modules/local/epytope_show_supported_models.nf
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Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
process EPYTOPE_SHOW_SUPPORTED_MODELS {
label 'process_low'

conda "bioconda::epytope=3.1.0"
conda "bioconda::epytope=3.3.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/epytope:3.1.0--pyh5e36f6f_0' :
'biocontainers/epytope:3.1.0--pyh5e36f6f_0' }"

'https://depot.galaxyproject.org/singularity/epytope:3.3.1--pyh7cba7a3_0' :
'quay.io/biocontainers/epytope:3.3.1--pyh7cba7a3_0' }"
input:
tuple val(meta), path(raw), path(software_versions)

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2 changes: 1 addition & 1 deletion modules/local/external_tools_import.nf
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Expand Up @@ -52,7 +52,7 @@ process EXTERNAL_TOOLS_IMPORT {
# Substitution 3: NMHOME should be the folder in which the tcsh script itself resides
#
sed -i.bak \
-e 's_bin/tcsh.*\$_usr/bin/env tcsh_' \
-e 's_bin/tcsh.*\$_opt/conda/bin/tcsh_' \
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Is this changed because of the container? Shouldn't this be container-unrelated?

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Good catch, that needs to be adjusted to the paths in the new container. That one was from the Conda-based container.

-e "s_/scratch_/tmp_" \
-e "s_setenv[[:space:]]NMHOME.*_setenv NMHOME \\`realpath -s \\\$0 | sed -r 's/[^/]+\$//'\\`_ " "${toolname}/${toolbinaryname}"

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6 changes: 3 additions & 3 deletions modules/local/get_prediction_versions.nf
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Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
process GET_PREDICTION_VERSIONS {
label 'process_low'

conda "bioconda::epytope=3.1.0"
conda "bioconda::epytope=3.3.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/epytope:3.1.0--pyh5e36f6f_0' :
'biocontainers/epytope:3.1.0--pyh5e36f6f_0' }"
'https://depot.galaxyproject.org/singularity/epytope:3.3.1--pyh7cba7a3_0' :
'quay.io/biocontainers/epytope:3.3.1--pyh7cba7a3_0' }"

input:
val external_tool_versions
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