From 4591ea2205d305d6bf27511571eb98ff7e4b9052 Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Mon, 9 May 2022 07:58:58 +0000
Subject: [PATCH] atomize

---
 modules/meryl/count/main.nf               | 14 ++-------
 modules/meryl/count/meta.yml              | 37 +++++++++--------------
 tests/modules/meryl/count/main.nf         |  2 +-
 tests/modules/meryl/count/nextflow.config |  1 -
 4 files changed, 18 insertions(+), 36 deletions(-)

diff --git a/modules/meryl/count/main.nf b/modules/meryl/count/main.nf
index 80491242..f7a2811d 100644
--- a/modules/meryl/count/main.nf
+++ b/modules/meryl/count/main.nf
@@ -11,15 +11,14 @@ process MERYL_COUNT {
     tuple val(meta), path(reads)
 
     output:
-    tuple val(meta), path("*.meryl"), emit: meryl
-    path "versions.yml"             , emit: versions
+    tuple val(meta), path("*.meryldb"), emit: meryl_db
+    path "versions.yml"               , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     for READ in $reads; do
@@ -27,15 +26,8 @@ process MERYL_COUNT {
             threads=$task.cpus \\
             $args \\
             $reads \\
-            output read.\${READ%.f*}.meryl
+            output read.\${READ%.f*}.meryldb
     done
-    meryl union-sum \\
-        threads=$task.cpus \\
-        $args2 \\
-        output ${prefix}.meryl
-
-    # clean up
-    rm -rf read.*.meryl
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/meryl/count/meta.yml b/modules/meryl/count/meta.yml
index 885267ec..dd59decd 100644
--- a/modules/meryl/count/meta.yml
+++ b/modules/meryl/count/meta.yml
@@ -1,51 +1,42 @@
 name: "meryl_count"
-## TODO nf-core: Add a description of the module and list keywords
-description: write your description here
+description: A genomic k-mer counter (and sequence utility) with nice features.
 keywords:
-  - sort
+  - k-mer
+  - count
 tools:
   - "meryl":
-      ## TODO nf-core: Add a description and other details for the software below
-      description: ""
-      homepage: "{}"
-      documentation: "{}"
-      tool_dev_url: "{}"
+      description: "A genomic k-mer counter (and sequence utility) with nice features. "
+      homepage: "https://github.com/marbl/meryl"
+      documentation: "https://meryl.readthedocs.io/en/latest/quick-start.html"
+      tool_dev_url: "https://github.com/marbl/meryl"
       doi: ""
       licence: "['GPL']"
 
-## TODO nf-core: Add a description of all of the variables used as input
 input:
-  # Only when we have meta
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  # 
-  ## TODO nf-core: Delete / customise this example input
-  - bam:
+  - reads:
       type: file
-      description: BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
+      description: |
+        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+        respectively.
 
-## TODO nf-core: Add a description of all of the variables used as output
 output:
-  #Only when we have meta
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  # 
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  ## TODO nf-core: Delete / customise this example output
-  - bam:
-      type: file
-      description: Sorted BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
+  - meryl_db:
+      type: directory
+      description: A Meryl k-mer database
 
 authors:
   - "@mahesh-panchal"
diff --git a/tests/modules/meryl/count/main.nf b/tests/modules/meryl/count/main.nf
index 8706046a..7d65b7dd 100644
--- a/tests/modules/meryl/count/main.nf
+++ b/tests/modules/meryl/count/main.nf
@@ -4,7 +4,7 @@ nextflow.enable.dsl = 2
 
 include { MERYL_COUNT } from '../../../../modules/meryl/count/main.nf'
 
-workflow test_meryl_count_single_end {
+workflow test_meryl_count {
 
     input = [
         [ id:'test' ], // meta map
diff --git a/tests/modules/meryl/count/nextflow.config b/tests/modules/meryl/count/nextflow.config
index 99e1f846..6d899c50 100644
--- a/tests/modules/meryl/count/nextflow.config
+++ b/tests/modules/meryl/count/nextflow.config
@@ -2,6 +2,5 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
     ext.args = 'k=21'
-    ext.args2 = 'k=21'
 
 }