Minor updates

nf-core · Jan 12, 2024 · 227af28 · 227af28
1 parent 8fb0ae0
commit 227af28
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Showing 3 changed files with 12 additions and 5 deletions.
diff --git a/modules/local/edger_qc.nf b/modules/local/edger_qc.nf
@@ -1,7 +1,7 @@
 process EDGER_QC {
     label 'process_medium'
 
-    conda 'bioconda::bioconductor-limma=3.50.0 bioconda::bioconductor-edger=3.36.0 conda-forge::r-data.table=1.14.2 conda-forge::r-gplots=3.1.1 conda-forge::r-statmod=1.4.36'
+    conda 'bioconda::bioconductor-limma=3.58.1 bioconda::bioconductor-edger=4.0.2 conda-forge::r-data.table=1.14.10 conda-forge::r-gplots=3.1.3 conda-forge::r-statmod=1.5.0'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-419bd7f10b2b902489ac63bbaafc7db76f8e0ae1:709335c37934db1b481054cbec637c6e5b5971cb-0' :
         'biocontainers/mulled-v2-419bd7f10b2b902489ac63bbaafc7db76f8e0ae1:709335c37934db1b481054cbec637c6e5b5971cb-0' }"

diff --git a/modules/local/mirdeep2_prepare.nf b/modules/local/mirdeep2_prepare.nf
@@ -3,10 +3,10 @@ process MIRDEEP2_PIGZ {
     tag "$meta.id"
 
     // TODO maybe create a mulled container and uncompress within mirdeep2_mapper?
-    conda 'bioconda::bioconvert=0.4.3'
+    conda 'bioconda::bioconvert=1.1.1'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconvert:0.4.3--py_0' :
-        'biocontainers/bioconvert:0.4.3--py_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconvert:1.1.1--pyhdfd78af_0' :
+        'biocontainers/bioconvert:1.1.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(reads)

diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf
@@ -72,6 +72,7 @@ include { MIRNA_QUANT           } from '../subworkflows/local/mirna_quant'
 include { GENOME_QUANT          } from '../subworkflows/local/genome_quant'
 include { MIRTRACE              } from '../subworkflows/local/mirtrace'
 include { MIRDEEP2              } from '../subworkflows/local/mirdeep2'
+include { INDEX_GENOME          } from '../../modules/local/bowtie_genome'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -157,9 +158,15 @@ workflow SMRNASEQ {
     if (params.with_umi){
         if (params.fasta){
             fasta_ch = file(params.fasta)
+
+            //This needs to be done here as GENOME_QUANT should not run prior to the deduplication of UMIs.
+            INDEX_GENOME ( fasta )
+
+            ch_versions = ch_versions.mix(INDEX_GENOME.out.versions)
+
             DEDUPLICATE_UMIS (
                 fasta_ch,
-                bt_index,
+                INDEX_GENOME.out.bowtie_indices,
                 FASTQC_UMITOOLS_FASTP.out.trim_reads
             )
             reads_for_mirna = DEDUPLICATE_UMIS.out.reads