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Merge pull request #208 from erikrikarddaniel/fix-tidyverse-version
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Updated modules to use the latest tidyverse env
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@danilodileo
danilodileo authored Nov 3, 2023
2 parents 55586b3 + fbbdb6b commit d95970a
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Showing 8 changed files with 24 additions and 24 deletions.
6 changes: 3 additions & 3 deletions modules/local/collect_featurecounts.nf
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Expand Up @@ -2,10 +2,10 @@ process COLLECT_FEATURECOUNTS {
tag "$meta.id"
label 'process_high'

conda "conda-forge::r-tidyverse=1.3.1 conda-forge::r-data.table=1.14.0 conda-forge::r-dtplyr=1.1.0"
conda "conda-forge::r-tidyverse=2.0.0 conda-forge::r-dtplyr=1.3.1 conda-forge::r-data.table=1.14.8"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-508c9bc5e929a77a9708902b1deca248c0c84689:0bb5bee2557136d28549f41d3faa08485e967aa1-0' :
'biocontainers/mulled-v2-508c9bc5e929a77a9708902b1deca248c0c84689:0bb5bee2557136d28549f41d3faa08485e967aa1-0' }"
'https://depot.galaxyproject.org/singularity/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1' :
'biocontainers/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1' }"

input:
tuple val(meta), path(inputfiles)
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6 changes: 3 additions & 3 deletions modules/local/collect_stats.nf
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Expand Up @@ -2,10 +2,10 @@ process COLLECT_STATS {
tag "$meta.id"
label 'process_low'

conda "conda-forge::r-tidyverse=1.3.1 conda-forge::r-data.table=1.14.0 conda-forge::r-dtplyr=1.1.0"
conda "conda-forge::r-tidyverse=2.0.0 conda-forge::r-dtplyr=1.3.1 conda-forge::r-data.table=1.14.8"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-508c9bc5e929a77a9708902b1deca248c0c84689:0bb5bee2557136d28549f41d3faa08485e967aa1-0' :
'biocontainers/mulled-v2-508c9bc5e929a77a9708902b1deca248c0c84689:0bb5bee2557136d28549f41d3faa08485e967aa1-0' } "
'https://depot.galaxyproject.org/singularity/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1' :
'biocontainers/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1' }"

input:
tuple val(meta), val(samples), path(trimlogs), path(bblogs), path(idxstats), path(fcs), path(mergetab)
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6 changes: 3 additions & 3 deletions modules/local/eggnog/sum.nf
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Expand Up @@ -2,10 +2,10 @@ process EGGNOG_SUM {
tag "$meta.id"
label 'process_low'

conda "conda-forge::r-tidyverse=1.3.1 conda-forge::r-data.table=1.14.0 conda-forge::r-dtplyr=1.1.0"
conda "conda-forge::r-tidyverse=2.0.0 conda-forge::r-dtplyr=1.3.1 conda-forge::r-data.table=1.14.8"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-508c9bc5e929a77a9708902b1deca248c0c84689:0bb5bee2557136d28549f41d3faa08485e967aa1-0' :
'biocontainers/mulled-v2-508c9bc5e929a77a9708902b1deca248c0c84689:0bb5bee2557136d28549f41d3faa08485e967aa1-0' } "
'https://depot.galaxyproject.org/singularity/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1' :
'biocontainers/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1' }"

input:

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6 changes: 3 additions & 3 deletions modules/local/format_tax.nf
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Expand Up @@ -2,10 +2,10 @@ process FORMAT_TAX {
tag "$meta.id"
label 'process_low'

conda "conda-forge::r-tidyverse=1.3.1 conda-forge::r-data.table=1.14.0 conda-forge::r-dtplyr=1.1.0"
conda "conda-forge::r-tidyverse=2.0.0 conda-forge::r-dtplyr=1.3.1 conda-forge::r-data.table=1.14.8"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-508c9bc5e929a77a9708902b1deca248c0c84689:0bb5bee2557136d28549f41d3faa08485e967aa1-0' :
'biocontainers/mulled-v2-508c9bc5e929a77a9708902b1deca248c0c84689:0bb5bee2557136d28549f41d3faa08485e967aa1-0' }"
'https://depot.galaxyproject.org/singularity/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1' :
'biocontainers/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1' }"

input:
tuple val(meta), path(taxtable)
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6 changes: 3 additions & 3 deletions modules/local/hmmrank.nf
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Expand Up @@ -2,10 +2,10 @@ process HMMRANK {
tag "$meta.id"
label 'process_low'

conda "conda-forge::r-tidyverse=1.3.1 conda-forge::r-data.table=1.14.0 conda-forge::r-dtplyr=1.1.0"
conda "conda-forge::r-tidyverse=2.0.0 conda-forge::r-dtplyr=1.3.1 conda-forge::r-data.table=1.14.8"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-508c9bc5e929a77a9708902b1deca248c0c84689:0bb5bee2557136d28549f41d3faa08485e967aa1-0' :
'biocontainers/mulled-v2-508c9bc5e929a77a9708902b1deca248c0c84689:0bb5bee2557136d28549f41d3faa08485e967aa1-0' } "
'https://depot.galaxyproject.org/singularity/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1' :
'biocontainers/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1' }"

input:
tuple val(meta), path(hmmtargsums)
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6 changes: 3 additions & 3 deletions modules/local/merge_summary_tables.nf
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Expand Up @@ -2,10 +2,10 @@ process MERGE_TABLES {
tag "$meta.id"
label 'process_low'

conda "conda-forge::r-tidyverse=1.3.1 conda-forge::r-data.table=1.14.0 conda-forge::r-dtplyr=1.1.0"
conda "conda-forge::r-tidyverse=2.0.0 conda-forge::r-dtplyr=1.3.1 conda-forge::r-data.table=1.14.8"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-508c9bc5e929a77a9708902b1deca248c0c84689:0bb5bee2557136d28549f41d3faa08485e967aa1-0' :
'biocontainers/mulled-v2-508c9bc5e929a77a9708902b1deca248c0c84689:0bb5bee2557136d28549f41d3faa08485e967aa1-0' } "
'https://depot.galaxyproject.org/singularity/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1' :
'biocontainers/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1' }"

input:

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6 changes: 3 additions & 3 deletions modules/local/sum_kofamscan.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,10 @@ process SUM_KOFAMSCAN {
tag "$meta.id"
label 'process_low'

conda "conda-forge::r-tidyverse=1.3.1 conda-forge::r-data.table=1.14.0 conda-forge::r-dtplyr=1.1.0"
conda "conda-forge::r-tidyverse=2.0.0 conda-forge::r-dtplyr=1.3.1 conda-forge::r-data.table=1.14.8"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-508c9bc5e929a77a9708902b1deca248c0c84689:0bb5bee2557136d28549f41d3faa08485e967aa1-0' :
'biocontainers/mulled-v2-508c9bc5e929a77a9708902b1deca248c0c84689:0bb5bee2557136d28549f41d3faa08485e967aa1-0' } "
'https://depot.galaxyproject.org/singularity/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1' :
'biocontainers/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1' }"

input:

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6 changes: 3 additions & 3 deletions modules/local/sum_taxonomy.nf
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Expand Up @@ -2,10 +2,10 @@ process SUM_TAXONOMY {
tag "$meta.id"
label 'process_low'

conda "conda-forge::r-tidyverse=1.3.1 conda-forge::r-data.table=1.14.0 conda-forge::r-dtplyr=1.1.0"
conda "conda-forge::r-tidyverse=2.0.0 conda-forge::r-dtplyr=1.3.1 conda-forge::r-data.table=1.14.8"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-508c9bc5e929a77a9708902b1deca248c0c84689:0bb5bee2557136d28549f41d3faa08485e967aa1-0' :
'biocontainers/mulled-v2-508c9bc5e929a77a9708902b1deca248c0c84689:0bb5bee2557136d28549f41d3faa08485e967aa1-0' } "
'https://depot.galaxyproject.org/singularity/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1' :
'biocontainers/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1' }"

input:

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