Merge branch 'master' into get_tbi_files_from_gatk4_mergevcfs

modules/bamtools/convert/meta.yml

@@ -42,7 +42,6 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  ## TODO nf-core: Delete / customise this example output
   - out:
       type: file
       description: The data in the asked format (bed, fasta, fastq, json, pileup, sam, yaml)

modules/bcftools/concat/main.nf

@@ -8,7 +8,7 @@ process BCFTOOLS_CONCAT {
         'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
 
     input:
-    tuple val(meta), path(vcfs)
+    tuple val(meta), path(vcfs), path(tbi)
 
     output:
     tuple val(meta), path("*.gz"), emit: vcf

modules/bcftools/concat/meta.yml

@@ -25,6 +25,11 @@ input:
       description: |
         List containing 2 or more vcf files
         e.g. [ 'file1.vcf', 'file2.vcf' ]
+  - tbi:
+      type: files
+      description: |
+        List containing 2 or more index files (optional)
+        e.g. [ 'file1.tbi', 'file2.tbi' ]
 output:
   - meta:
       type: map

modules/filtlong/main.nf

@@ -20,7 +20,7 @@ process FILTLONG {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def short_reads = meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
+    def short_reads = !shortreads ? "" : meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
     """
     filtlong \\
         $short_reads \\

tests/modules/bcftools/concat/main.nf

@@ -4,13 +4,25 @@ nextflow.enable.dsl = 2
 
 include { BCFTOOLS_CONCAT } from '../../../../modules/bcftools/concat/main.nf'
 
-workflow test_bcftools_concat {
+workflow test_bcftools_concat_tbi {
     
     input = [ [ id:'test3' ], // meta map
               [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) ]
+                file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) ],
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true) ]
+            ]
+
+    BCFTOOLS_CONCAT ( input )
+}
+
+workflow test_bcftools_concat_no_tbi {
+    
+    input = [ [ id:'test3' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) ],
+              []
             ]
 
-
     BCFTOOLS_CONCAT ( input )
 }

tests/modules/bcftools/concat/test.yml

@@ -1,8 +1,17 @@
-- name: bcftools concat test_bcftools_concat
-  command: nextflow run ./tests/modules/bcftools/concat -entry test_bcftools_concat -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/concat/nextflow.config
+- name: bcftools concat test_bcftools_concat_tbi
+  command: nextflow run ./tests/modules/bcftools/concat -entry test_bcftools_concat_tbi -c ./tests/config/nextflow.config  -c ./tests/modules/bcftools/concat/nextflow.config
   tags:
-    - bcftools/concat
     - bcftools
+    - bcftools/concat
+  files:
+    - path: output/bcftools/test3.vcf.gz
+      md5sum: 35c88bfaad20101062e98beb217d7137
+
+- name: bcftools concat test_bcftools_concat_no_tbi
+  command: nextflow run ./tests/modules/bcftools/concat -entry test_bcftools_concat_no_tbi -c ./tests/config/nextflow.config  -c ./tests/modules/bcftools/concat/nextflow.config
+  tags:
+    - bcftools
+    - bcftools/concat
   files:
     - path: output/bcftools/test3.vcf.gz
       md5sum: 35c88bfaad20101062e98beb217d7137

tests/modules/filtlong/nextflow.config

@@ -2,4 +2,6 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
+    ext.args = "--min_length 10"
+
 }

tests/modules/filtlong/test.yml

@@ -1,23 +1,26 @@
 - name: filtlong test_filtlong
-  command: nextflow run ./tests/modules/filtlong -entry test_filtlong -c ./tests/config/nextflow.config -c ./tests/modules/filtlong/nextflow.config
+  command: nextflow run ./tests/modules/filtlong -entry test_filtlong -c ./tests/config/nextflow.config  -c ./tests/modules/filtlong/nextflow.config
   tags:
     - filtlong
   files:
     - path: output/filtlong/test_lr_filtlong.fastq.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
+      contains:
+        - "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"
 
 - name: filtlong test_filtlong_illumina_se
-  command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_se -c ./tests/config/nextflow.config -c ./tests/modules/filtlong/nextflow.config
+  command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_se -c ./tests/config/nextflow.config  -c ./tests/modules/filtlong/nextflow.config
   tags:
     - filtlong
   files:
     - path: output/filtlong/test_lr_filtlong.fastq.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
+      contains:
+        - "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"
 
 - name: filtlong test_filtlong_illumina_pe
-  command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_pe -c ./tests/config/nextflow.config -c ./tests/modules/filtlong/nextflow.config
+  command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_pe -c ./tests/config/nextflow.config  -c ./tests/modules/filtlong/nextflow.config
   tags:
     - filtlong
   files:
     - path: output/filtlong/test_lr_filtlong.fastq.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
+      contains:
+        - "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"