# HG changeset patch
# User kkonganti
# Date 1701203211 18000
# Node ID 5eaaf749472cf2fbcb7c283324d241dafd538128
# Parent  d8913a37810ac4ee65b61ff1121a1f901eed850d
"planemo upload"

diff -r d8913a37810a -r 5eaaf749472c 0.1.0/modules/multiqc/main.nf
--- a/0.1.0/modules/multiqc/main.nf	Mon Nov 27 20:49:25 2023 -0500
+++ b/0.1.0/modules/multiqc/main.nf	Tue Nov 28 15:26:51 2023 -0500
@@ -3,7 +3,7 @@
     tag 'MultiQC'
 
     module (params.enable_module ? "${params.swmodulepath}${params.fs}multiqc${params.fs}1.14" : null)
-    conda (params.enable_conda ? 'bioconda::multiqc=1.14 conda-forge::spectra conda-forge::lzstring conda-forge::imp' : null)
+    conda (params.enable_conda ? 'bioconda::multiqc=1.14 conda-forge::python=3.11 conda-forge::spectra conda-forge::lzstring conda-forge::imp' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
         'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
diff -r d8913a37810a -r 5eaaf749472c 0.1.0/workflows/cronology.nf
--- a/0.1.0/workflows/cronology.nf	Mon Nov 27 20:49:25 2023 -0500
+++ b/0.1.0/workflows/cronology.nf	Tue Nov 28 15:26:51 2023 -0500
@@ -203,7 +203,11 @@
                 .set { ch_assembly }
 
             software_versions
-                .mix(POLYPOLISH.out.versions)
+                .mix( 
+                    BWA_IDX_MEM.out.versions,
+                    POLYPOLISH.out.versions
+                )
+                .set { software_versions }
         }
 
         ch_assembly
@@ -252,7 +256,8 @@
             )
 
             software_versions
-                .mix(PIRATE.out.versions)
+                .mix( PIRATE.out.versions )
+                .set { software_versions }
         }
 
         RMLST_POST.out.tsv