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Merge branch 'dev' into combgc_new_input_param
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@jasmezz
jasmezz committed Apr 21, 2023
2 parents 9986687 + c955fac commit e381fbe
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2 changes: 1 addition & 1 deletion CHANGELOG.md
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Expand Up @@ -13,7 +13,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#251](https://github.com/nf-core/funcscan/pull/251) Added annotation tool: Pyrodigal. (by @jasmezz)
- [#252](https://github.com/nf-core/funcscan/pull/252) Added a new parameter `-arg_rgi_savejson` that saves the file `<samplename>.json` in the RGI directory. The default ouput for RGI is now only `<samplename>.txt`. (by @darcy220606)
- [#253](https://github.com/nf-core/funcscan/pull/253) Updated Prodigal to have compressed output files. (by @jasmezz)
- [#258](https://github.com/nf-core/funcscan/pull/258) Added comBGC function to screen whole directory of antiSMASH output (one subfolder per sample). (by @jasmezz)

### `Fixed`

Expand All @@ -23,6 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#235](https://github.com/nf-core/funcscan/pull/235) Renamed parameter `annotation_bakta_db` to `annotation_bakta_db_localpath`. (by @jasmezz)
- [#242](https://github.com/nf-core/funcscan/pull/242) Fixed MACREL '.faa' issue that was generated when it was run on its own and upgraded MACREL from version `1.1.0` to `1.2.0` (by @Darcy220606)
- [#248](https://github.com/nf-core/funcscan/pull/248) Applied best-practice `error("message")` to all (sub)workflow files. (by @jasmezz)
- [#254](https://github.com/nf-core/funcscan/pull/254) Further resource optimisation based on feedback from 'real world' datasets. (ongoing, reported by @alexhbnr and @Darcy220606, fix by @jfy133)

### `Dependencies`

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69 changes: 38 additions & 31 deletions conf/base.config
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ process {
withLabel:process_high {
cpus = { check_max( 12 * task.attempt, 'cpus' ) }
memory = { check_max( 72.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}
withLabel:process_long {
time = { check_max( 20.h * task.attempt, 'time' ) }
Expand All @@ -67,12 +67,12 @@ process {
*/

withName: GUNZIP {
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
memory = { check_max( 2.GB * task.attempt, 'memory' ) }
cpus = 1
}

withName: UNTAR {
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
memory = { check_max( 2.GB * task.attempt, 'memory' ) }
cpus = 1
}

Expand All @@ -81,49 +81,55 @@ process {
}

withName: PROKKA {
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
}

withName: PRODIGAL_GFF {
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
memory = { check_max( 2.GB * task.attempt, 'memory' ) }
cpus = 1
}

withName: PRODIGAL_GBK {
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
memory = { check_max( 2.GB * task.attempt, 'memory' ) }
cpus = 1
}

withName: BAKTA {
memory = { check_max( 64.GB * task.attempt, 'memory' ) }
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
}

withName: ABRICATE_RUN {
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 2.GB * task.attempt, 'memory' ) }
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
}

withName: AMRFINDERPLUS_RUN {
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
memory = { check_max( 2.GB * task.attempt, 'memory' ) }
cpus = 1
}

withName: DEEPARG_DOWNLOADDATA {
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
memory = { check_max( 2.GB * task.attempt, 'memory' ) }
cpus = 1
}

withName: DEEPARG_PREDICT {
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
memory = { check_max( 2.GB * task.attempt, 'memory' ) }
cpus = 1
}

withName: FARGENE {
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 2.GB * task.attempt, 'memory' ) }
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
}

withName: RGI_MAIN {
memory = { check_max( 12.GB * task.attempt, 'memory' ) }
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 28.GB * task.attempt, 'memory' ) }
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
}

withName: AMPIR {
Expand All @@ -132,28 +138,28 @@ process {
}

withName: AMPLIFY_PREDICT {
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
cpus = 1
time = { check_max( 8.h * task.attempt, 'time' ) }
time = { check_max( 24.h * task.attempt, 'time' ) }
}

withName: AMP_HMMER_HMMSEARCH {
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 2.GB * task.attempt, 'memory' ) }
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
}

withName: MACREL_CONTIGS {
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
}

withName: BGC_HMMER_HMMSEARCH {
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 2.GB * task.attempt, 'memory' ) }
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
}

withName: ANTISMASH_ANTISMASHLITE {
memory = { check_max( 64.GB * task.attempt, 'memory' ) }
memory = { check_max( 64.GB * task.attempt, 'memory' ) }
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
time = { check_max( 12.h * task.attempt, 'time' ) }
}
Expand All @@ -164,19 +170,19 @@ process {
}

withName: DEEPBGC_DOWNLOAD {
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
memory = { check_max( 2.GB * task.attempt, 'memory' ) }
cpus = 1
}

withName: DEEPBGC_PIPELINE {
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
memory = { check_max( 2.GB * task.attempt, 'memory' ) }
cpus = 1
time = { check_max( 12.h * task.attempt, 'time' ) }
time = { check_max( 24.h * task.attempt, 'time' ) }
}

withName: GECCO_RUN {
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
}

withName: HAMRONIZATION_ABRICATE {
Expand All @@ -190,7 +196,7 @@ process {
}

withName: HAMRONIZATION_DEEPARG {
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
cpus = 1
}

Expand All @@ -211,5 +217,6 @@ process {

withName: AMPCOMBI {
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 2.h * task.attempt, 'time' ) }
}
}

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