fix report parameter and update docker image

fmalmeida · Jul 7, 2024 · 91471f2 · 91471f2
1 parent d6d28b0
commit 91471f2
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Showing 6 changed files with 4 additions and 9 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
       )