ebi-metagen module patch

modules.json

@@ -2,7 +2,7 @@
     "name": "ebi-metagenomics/miassembler",
     "homePage": "https://github.com/ebi-metagenomics/miassembler",
     "repos": {
-        "git@github.com:EBI-Metagenomics/nf-modules.git": {
+        "https://github.com/EBI-Metagenomics/nf-modules": {
             "modules": {
                 "ebi-metagenomics": {
                     "bwamem2/mem": {
@@ -13,7 +13,8 @@
                     "samtools/bam2fq": {
                         "branch": "main",
                         "git_sha": "88f2bfbe6f0ba858d0833db590e647c4678656a7",
-                        "installed_by": ["reads_bwamem2_decontamination"]
+                        "installed_by": ["reads_bwamem2_decontamination"],
+                        "patch": "modules/ebi-metagenomics/samtools/bam2fq/samtools-bam2fq.diff"
                     }
                 }
             },

modules/ebi-metagenomics/bwamem2/mem/environment.yml

@@ -1,10 +1,11 @@
 name: bwamem2_mem
+
 channels:
   - conda-forge
   - bioconda
   - defaults
+
 dependencies:
   - bwa-mem2=2.2.1
-  # renovate: datasource=conda depName=bioconda/samtools
-  - samtools=1.19.2
   - htslib=1.19.1
+  - samtools=1.19.2

modules/ebi-metagenomics/samtools/bam2fq/samtools-bam2fq.diff

@@ -0,0 +1,14 @@
+Changes in module 'ebi-metagenomics/samtools/bam2fq'
+--- modules/ebi-metagenomics/samtools/bam2fq/main.nf
++++ modules/ebi-metagenomics/samtools/bam2fq/main.nf
+@@ -21,7 +21,7 @@
+
+     script:
+     def args = task.ext.args ?: ''
+-    def prefix = task.ext.prefix ?: "${meta.id}"
++    def prefix = task.ext.prefix ? "${task.ext.prefix}_${meta.id}": "${meta.id}"
+
+     if (split) {
+         """
+
+************************************************************