Patch modules to fix nf-core#1103

drpatelh · Jan 3, 2024 · a59a6f3 · a59a6f3
1 parent c261e9c
commit a59a6f3
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Showing 9 changed files with 118 additions and 13 deletions.
diff --git a/modules.json b/modules.json
@@ -28,12 +28,14 @@
                     "fastp": {
                         "branch": "master",
                         "git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd",
-                        "installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
+                        "installed_by": ["fastq_fastqc_umitools_fastp", "modules"],
+                        "patch": "modules/nf-core/fastp/fastp.diff"
                     },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "102cc9b709a6da9f7cee2373563ab1464fca9c0a",
-                        "installed_by": ["fastq_fastqc_umitools_trimgalore", "fastq_fastqc_umitools_fastp"]
+                        "installed_by": ["fastq_fastqc_umitools_trimgalore", "fastq_fastqc_umitools_fastp"],
+                        "patch": "modules/nf-core/fastqc/fastqc.diff"
                     },
                     "fq/subsample": {
                         "branch": "master",
@@ -222,12 +224,14 @@
                     "umitools/dedup": {
                         "branch": "master",
                         "git_sha": "7297204bf49273300a3dbfa4b7a4027c8683f1bd",
-                        "installed_by": ["bam_dedup_stats_samtools_umitools"]
+                        "installed_by": ["bam_dedup_stats_samtools_umitools"],
+                        "patch": "modules/nf-core/umitools/dedup/umitools-dedup.diff"
                     },
                     "umitools/extract": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"]
+                        "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"],
+                        "patch": "modules/nf-core/umitools/extract/umitools-extract.diff"
                     },
                     "untar": {
                         "branch": "master",

diff --git a/modules/nf-core/fastp/fastp.diff b/modules/nf-core/fastp/fastp.diff
diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf
diff --git a/modules/nf-core/fastqc/fastqc.diff b/modules/nf-core/fastqc/fastqc.diff
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
diff --git a/modules/nf-core/umitools/dedup/main.nf b/modules/nf-core/umitools/dedup/main.nf
diff --git a/modules/nf-core/umitools/dedup/umitools-dedup.diff b/modules/nf-core/umitools/dedup/umitools-dedup.diff
diff --git a/modules/nf-core/umitools/extract/main.nf b/modules/nf-core/umitools/extract/main.nf
diff --git a/modules/nf-core/umitools/extract/umitools-extract.diff b/modules/nf-core/umitools/extract/umitools-extract.diff