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jasmezzjasmezz
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Merge branch 'dev' into combgc_new_input_param
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‎CHANGELOG.md

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Original file line numberDiff line numberDiff line change
@@ -13,7 +13,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- [#251](https://github.com/nf-core/funcscan/pull/251) Added annotation tool: Pyrodigal. (by @jasmezz)
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- [#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)
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- [#253](https://github.com/nf-core/funcscan/pull/253) Updated Prodigal to have compressed output files. (by @jasmezz)
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- [#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)
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### `Fixed`
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@@ -23,6 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- [#235](https://github.com/nf-core/funcscan/pull/235) Renamed parameter `annotation_bakta_db` to `annotation_bakta_db_localpath`. (by @jasmezz)
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- [#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)
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- [#248](https://github.com/nf-core/funcscan/pull/248) Applied best-practice `error("message")` to all (sub)workflow files. (by @jasmezz)
25+
- [#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)
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### `Dependencies`
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‎conf/base.config

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Original file line numberDiff line numberDiff line change
@@ -43,7 +43,7 @@ process {
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withLabel:process_high {
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cpus = { check_max( 12 * task.attempt, 'cpus' ) }
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memory = { check_max( 72.GB * task.attempt, 'memory' ) }
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time = { check_max( 1.h * task.attempt, 'time' ) }
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time = { check_max( 1.h * task.attempt, 'time' ) }
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}
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withLabel:process_long {
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time = { check_max( 20.h * task.attempt, 'time' ) }
@@ -67,12 +67,12 @@ process {
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*/
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withName: GUNZIP {
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memory = { check_max( 1.GB * task.attempt, 'memory' ) }
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memory = { check_max( 2.GB * task.attempt, 'memory' ) }
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cpus = 1
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}
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withName: UNTAR {
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memory = { check_max( 1.GB * task.attempt, 'memory' ) }
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memory = { check_max( 2.GB * task.attempt, 'memory' ) }
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cpus = 1
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}
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@@ -81,49 +81,55 @@ process {
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}
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withName: PROKKA {
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memory = { check_max( 4.GB * task.attempt, 'memory' ) }
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cpus = { check_max( 4 * task.attempt, 'cpus' ) }
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time = { check_max( 8.h * task.attempt, 'time' ) }
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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cpus = { check_max( 4 * task.attempt, 'cpus' ) }
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time = { check_max( 8.h * task.attempt, 'time' ) }
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}
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withName: PRODIGAL_GFF {
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memory = { check_max( 1.GB * task.attempt, 'memory' ) }
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memory = { check_max( 2.GB * task.attempt, 'memory' ) }
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cpus = 1
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}
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withName: PRODIGAL_GBK {
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memory = { check_max( 1.GB * task.attempt, 'memory' ) }
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memory = { check_max( 2.GB * task.attempt, 'memory' ) }
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cpus = 1
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}
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withName: BAKTA {
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memory = { check_max( 64.GB * task.attempt, 'memory' ) }
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cpus = { check_max( 8 * task.attempt, 'cpus' ) }
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time = { check_max( 8.h * task.attempt, 'time' ) }
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}
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withName: ABRICATE_RUN {
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memory = { check_max( 1.GB * task.attempt, 'memory' ) }
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cpus = { check_max( 4 * task.attempt, 'cpus' ) }
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memory = { check_max( 2.GB * task.attempt, 'memory' ) }
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cpus = { check_max( 4 * task.attempt, 'cpus' ) }
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}
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withName: AMRFINDERPLUS_RUN {
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memory = { check_max( 1.GB * task.attempt, 'memory' ) }
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memory = { check_max( 2.GB * task.attempt, 'memory' ) }
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cpus = 1
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}
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withName: DEEPARG_DOWNLOADDATA {
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memory = { check_max( 1.GB * task.attempt, 'memory' ) }
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memory = { check_max( 2.GB * task.attempt, 'memory' ) }
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cpus = 1
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}
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withName: DEEPARG_PREDICT {
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memory = { check_max( 1.GB * task.attempt, 'memory' ) }
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memory = { check_max( 2.GB * task.attempt, 'memory' ) }
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cpus = 1
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}
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withName: FARGENE {
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memory = { check_max( 1.GB * task.attempt, 'memory' ) }
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cpus = { check_max( 4 * task.attempt, 'cpus' ) }
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memory = { check_max( 2.GB * task.attempt, 'memory' ) }
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cpus = { check_max( 4 * task.attempt, 'cpus' ) }
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}
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withName: RGI_MAIN {
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memory = { check_max( 12.GB * task.attempt, 'memory' ) }
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cpus = { check_max( 4 * task.attempt, 'cpus' ) }
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memory = { check_max( 28.GB * task.attempt, 'memory' ) }
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cpus = { check_max( 4 * task.attempt, 'cpus' ) }
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}
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withName: AMPIR {
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}
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withName: AMPLIFY_PREDICT {
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memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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cpus = 1
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time = { check_max( 8.h * task.attempt, 'time' ) }
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time = { check_max( 24.h * task.attempt, 'time' ) }
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}
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withName: AMP_HMMER_HMMSEARCH {
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memory = { check_max( 1.GB * task.attempt, 'memory' ) }
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cpus = { check_max( 4 * task.attempt, 'cpus' ) }
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memory = { check_max( 2.GB * task.attempt, 'memory' ) }
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cpus = { check_max( 4 * task.attempt, 'cpus' ) }
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}
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withName: MACREL_CONTIGS {
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memory = { check_max( 4.GB * task.attempt, 'memory' ) }
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cpus = { check_max( 4 * task.attempt, 'cpus' ) }
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cpus = { check_max( 4 * task.attempt, 'cpus' ) }
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}
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withName: BGC_HMMER_HMMSEARCH {
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memory = { check_max( 1.GB * task.attempt, 'memory' ) }
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cpus = { check_max( 4 * task.attempt, 'cpus' ) }
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memory = { check_max( 2.GB * task.attempt, 'memory' ) }
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cpus = { check_max( 4 * task.attempt, 'cpus' ) }
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}
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withName: ANTISMASH_ANTISMASHLITE {
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memory = { check_max( 64.GB * task.attempt, 'memory' ) }
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memory = { check_max( 64.GB * task.attempt, 'memory' ) }
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cpus = { check_max( 8 * task.attempt, 'cpus' ) }
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time = { check_max( 12.h * task.attempt, 'time' ) }
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}
@@ -164,19 +170,19 @@ process {
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withName: DEEPBGC_DOWNLOAD {
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memory = { check_max( 1.GB * task.attempt, 'memory' ) }
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memory = { check_max( 2.GB * task.attempt, 'memory' ) }
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cpus = 1
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}
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withName: DEEPBGC_PIPELINE {
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memory = { check_max( 1.GB * task.attempt, 'memory' ) }
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memory = { check_max( 2.GB * task.attempt, 'memory' ) }
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cpus = 1
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time = { check_max( 12.h * task.attempt, 'time' ) }
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time = { check_max( 24.h * task.attempt, 'time' ) }
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}
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withName: GECCO_RUN {
178-
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
179-
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
184+
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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cpus = { check_max( 4 * task.attempt, 'cpus' ) }
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}
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withName: HAMRONIZATION_ABRICATE {
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}
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withName: HAMRONIZATION_DEEPARG {
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memory = { check_max( 4.GB * task.attempt, 'memory' ) }
199+
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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cpus = 1
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}
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@@ -211,5 +217,6 @@ process {
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withName: AMPCOMBI {
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
220+
time = { check_max( 2.h * task.attempt, 'time' ) }
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}
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}

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