diff --git a/CHANGELOG.md b/CHANGELOG.md index ffb4ae15..3d8fc04a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#514](https://github.com/nf-core/mag/pull/514) - Fix missing CONCOCT files in downstream output (reported by @maxibor, fix by @jfy133) - [#515](https://github.com/nf-core/mag/pull/515) - Fix overwriting of GUNC output directories when running with domain classification (reported by @maxibor, fix by @jfy133) - [#516](https://github.com/nf-core/mag/pull/516) - Fix edge-case bug where MEGAHIT re-uses previous work directory on resume and fails (reported by @husensofteng, fix by @prototaxites) +- [#520](https://github.com/nf-core/mag/pull/520) - Fix missing Tiara output files (fix by @jfy133) +- [#522](https://github.com/nf-core/mag/pull/522) - Fix 'nulls' in depth plot PNG files (fix by @jfy133) ### `Dependencies` diff --git a/conf/modules.config b/conf/modules.config index 33a19831..c87d71d9 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -698,17 +698,10 @@ process { withName: TIARA_TIARA { publishDir = [ - [ - path: { "${params.outdir}/Taxonomy/Tiara" }, + path: { "${params.outdir}/Taxonomy/Tiara/" }, mode: params.publish_dir_mode, - pattern: { "${meta.assembler}-${meta.id}.tiara.{txt}" } - ], - [ - path: { "${params.outdir}/Taxonomy/Tiara/log" }, - mode: params.publish_dir_mode, - pattern: { "log_${meta.assembler}-${meta.id}.tiara.{txt}" } + pattern: "*.txt" ] - ] ext.args = { "--min_len ${params.tiara_min_length} --probabilities" } ext.prefix = { "${meta.assembler}-${meta.id}.tiara" } } @@ -720,7 +713,7 @@ process { withName: TIARA_SUMMARY { publishDir = [ - path: { "${params.outdir}/Taxonomy/" }, + path: { "${params.outdir}/GenomeBinning/Tiara" }, mode: params.publish_dir_mode, pattern: "tiara_summary.tsv" ] diff --git a/docs/output.md b/docs/output.md index e78d244b..20cab1da 100644 --- a/docs/output.md +++ b/docs/output.md @@ -434,12 +434,12 @@ Tiara is a contig classifier that identifies the domain (prokarya, eukarya) of c - `Taxonomy/Tiara/` - `[assembler]-[sample/group].tiara.txt` - Tiara output classifications (with probabilities) for all contigs within the specified sample/group assembly - - `log/log_[assembler]-[sample/group].txt` - log file detailing the parameters used by the Tiara model for contig classification. + - `log_[assembler]-[sample/group].txt` - log file detailing the parameters used by the Tiara model for contig classification. - `GenomeBinning/tiara_summary.tsv` - Summary of Tiara domain classification for all bins. -Typically, you would use `tiara_summary.tsv` as the primary file to see which bins or unbins have been classified to which domains at a glance, whereas `[assembler]-[sample/group].tiara.txt` provides classifications for each contig. +Typically, you would use `tiara_summary.tsv` as the primary file to see which bins or unbins have been classified to which domains at a glance, whereas the files in `Taxonomy/Tiara` provide classifications for each contig. ### Bin sequencing depth diff --git a/modules/local/mag_depths_plot.nf b/modules/local/mag_depths_plot.nf index 150d96fa..5f2f44ea 100644 --- a/modules/local/mag_depths_plot.nf +++ b/modules/local/mag_depths_plot.nf @@ -11,14 +11,14 @@ process MAG_DEPTHS_PLOT { path(sample_groups) output: - tuple val(meta), path("${meta.assembler}-${meta.domain}-${meta.binner}-${meta.id}-binDepths.heatmap.png"), emit: heatmap + tuple val(meta), path("${meta.assembler}-${meta.binner}-${meta.id}-binDepths.heatmap.png"), emit: heatmap path "versions.yml" , emit: versions script: """ plot_mag_depths.py --bin_depths ${depths} \ --groups ${sample_groups} \ - --out "${meta.assembler}-${meta.domain}-${meta.binner}-${meta.id}-binDepths.heatmap.png" + --out "${meta.assembler}-${meta.binner}-${meta.id}-binDepths.heatmap.png" cat <<-END_VERSIONS > versions.yml "${task.process}":