From 91471f2e4821234359a7d8c15430c473787f74ea Mon Sep 17 00:00:00 2001 From: Felipe Almeida Date: Sun, 7 Jul 2024 07:17:53 -0300 Subject: [PATCH] fix report parameter and update docker image --- conf/docker.config | 2 +- conf/singularity.config | 2 +- docker/renv/reports/report_general.Rmd | 5 ++--- modules/generic/reports.nf | 2 -- modules/generic/sourmash_all.nf | 1 - workflows/bacannot.nf | 1 - 6 files changed, 4 insertions(+), 9 deletions(-) diff --git a/conf/docker.config b/conf/docker.config index 5b7db8a..7de1e86 100644 --- a/conf/docker.config +++ b/conf/docker.config @@ -24,7 +24,7 @@ process { // container for R tools withLabel: 'renv' { - container = 'fmalmeida/bacannot@sha256:1b284a6d6f7be942d714f912d863a1d86dfa465ef600931b9f08e609e2c9884d' + container = 'fmalmeida/bacannot@sha256:23a0713d3694a10ee4c570a4e65a471045781a73711495aa08ae7d40f9b65097' } // container for bacannot server diff --git a/conf/singularity.config b/conf/singularity.config index 2b16324..f05eb5d 100644 --- a/conf/singularity.config +++ b/conf/singularity.config @@ -27,7 +27,7 @@ process { // container for R tools withLabel: 'renv' { - container = 'docker://fmalmeida/bacannot@sha256:1b284a6d6f7be942d714f912d863a1d86dfa465ef600931b9f08e609e2c9884d' + container = 'docker://fmalmeida/bacannot@sha256:23a0713d3694a10ee4c570a4e65a471045781a73711495aa08ae7d40f9b65097' } // container for bacannot server diff --git a/docker/renv/reports/report_general.Rmd b/docker/renv/reports/report_general.Rmd index afb3568..54222a7 100644 --- a/docker/renv/reports/report_general.Rmd +++ b/docker/renv/reports/report_general.Rmd @@ -9,7 +9,6 @@ params: barrnap: mlst: refseq_masher: - sourmash_csv: sourmash_png: query: output: @@ -59,8 +58,8 @@ if (file.exists(params$kegg)) { } else { kegg_not_null <- FALSE } -sourmash_csv <- try(read.delim(params$sourmash_csv, header = TRUE), silent = TRUE) -if (file.exists(params$kegg)) { + +if (file.exists(params$sourmash_png)) { sourmash_not_null <- TRUE sourmash_png <- params$sourmash_png } else { diff --git a/modules/generic/reports.nf b/modules/generic/reports.nf index e55ce28..617174d 100644 --- a/modules/generic/reports.nf +++ b/modules/generic/reports.nf @@ -5,7 +5,6 @@ process REPORT { input: tuple val(prefix), file('annotation_stats.tsv'), file(gff), file(barrnap), file(mlst), file(keggsvg), file(refseq_masher_txt), file(amrfinder), file(rgi), file(rgi_parsed), file(rgi_heatmap), file(argminer_out), file(resfinder_tab), file(resfinder_point), file(resfinder_phenotable), file(vfdb_blastn), file(victors_blastp), file(phigaro_txt), file(phispy_tsv), file(iceberg_blastp), file(iceberg_blastn), file(plasmids_tsv), file(platon_tsv), file(mobsuite_tsv), file(gi_image), file(phast_blastp), file(digIS), file(integronfinder) - file(sourmash_csv) file(sourmash_png) output: @@ -32,7 +31,6 @@ process REPORT { barrnap = "$barrnap", \ mlst = "$mlst", \ refseq_masher = "$refseq_masher_txt", \ - sourmash_csv = "$sourmash_csv", \ sourmash_png = "$sourmash_png", \ query = "${prefix}" ) diff --git a/modules/generic/sourmash_all.nf b/modules/generic/sourmash_all.nf index b9d81e4..6ff7dc6 100644 --- a/modules/generic/sourmash_all.nf +++ b/modules/generic/sourmash_all.nf @@ -14,7 +14,6 @@ process SOURMASH_ALL { path "*" , emit: all path "sourmash_version.txt" , emit: versions path "sourmash_cmp.matrix.png" , emit: plot - path "sourmash_plot.csv" , emit: csv when: !params.skip_sourmash diff --git a/workflows/bacannot.nf b/workflows/bacannot.nf index 9a36807..4162d11 100644 --- a/workflows/bacannot.nf +++ b/workflows/bacannot.nf @@ -408,7 +408,6 @@ workflow BACANNOT { .join( phast_output_ch, remainder: true ) .join( MERGE_ANNOTATIONS.out.digis_gff ) .join( ch_integron_finder_gff, remainder: true ), - SOURMASH_ALL.out.csv.first(), // make value channel SOURMASH_ALL.out.plot.first() // make value channel )