Add fq2bam to methylseq

README.md

@@ -35,7 +35,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 The pipeline allows you to choose between running either [Bismark](https://github.com/FelixKrueger/Bismark), [bwa-meth](https://github.com/brentp/bwa-meth) / [MethylDackel](https://github.com/dpryan79/methyldackel) or [BWA-Mem](https://github.com/lh3/bwa) plus [rastair](https://bitbucket.org/bsblabludwig/rastair/src/master/) for TAPS data processing. rastair can also be used with bwa-meth aligned reads by setting the aligner to `--aligner bwameth` and adding the flag `--taps`.
 
-Choose between workflows by using `--aligner bismark` (default, uses bowtie2 for alignment), `--aligner bismark_hisat`, `--aligner bwameth` or `--aligner bwamem`. For higher performance, the pipeline can leverage the [Parabricks implementation of bwa-meth (fq2bammeth)](https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/man_fq2bam_meth.html) and the [Parabricks implementation of bwa-mem (fq2bammemh)](https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/man_fq2bam.html), which implement the baseline tools `bwa-meth` and `bwa-mem`. To use this option, include the `gpu` profile along with `--aligner bwameth` or `--aligner bwamem`.
+Choose between workflows by using `--aligner bismark` (default, uses bowtie2 for alignment), `--aligner bismark_hisat`, `--aligner bwameth` or `--aligner bwamem`. For higher performance, the pipeline can leverage the [Parabricks implementation of bwa-meth (fq2bammeth)](https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/man_fq2bam_meth.html) and the [Parabricks implementation of bwa-mem (fq2bam)](https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/man_fq2bam.html), which implement the baseline tools `bwa-meth` and `bwa-mem`. To use this option, include the `gpu` profile along with `--aligner bwameth` or `--aligner bwamem`.
 
 Note: For faster CPU runs with BWA-Meth, enable the BWA-MEM2 algorithm using `--use_mem2`. The GPU pathway (Parabricks) requires `-profile gpu` and a container runtime (Docker, Singularity, or Podman); Conda/Mamba are not supported for the GPU module.
 

conf/modules/parabricks_fq2bam.config

@@ -0,0 +1,11 @@
+process {
+    withName: PARABRICKS_FQ2BAM {
+        cache = 'lenient' // This is set because in the module command the index files are touched so as to have bwameth not complain
+        publishDir = [
+                path: { "${params.outdir}/${params.aligner}/alignments" },
+                pattern: "*.bam",
+                mode: params.publish_dir_mode,
+                enabled: params.save_align_intermeds
+        ]
+    }
+}

conf/modules/parabricks_fq2bammeth.config

@@ -1,7 +1,6 @@
 process {
     withName: PARABRICKS_FQ2BAMMETH {
         cache = 'lenient' // This is set because in the module command the index files are touched so as to have bwameth not complain
-        ext.args = '--low-memory'
         publishDir = [
                 path: { "${params.outdir}/${params.aligner}/alignments" },
                 pattern: "*.bam",

conf/subworkflows/fastq_align_dedup_bwamem.config

@@ -1,4 +1,6 @@
+
 includeConfig "../modules/bwamem_align.config"
+includeConfig "../modules/parabricks_fq2bam.config"
 includeConfig "../modules/picard_addorreplacereadgroups.config"
 includeConfig "../modules/picard_markduplicates.config"
 includeConfig "../modules/samtools_stats.config"
@@ -35,16 +37,4 @@ process {
             ]
         ]
     }
-
-    // SAMTOOLS_INDEX after PICARD_MARKDUPLICATES - publish to deduplicated when deduplication runs
-    withName: 'NFCORE_METHYLSEQ:METHYLSEQ:FASTQ_ALIGN_DEDUP_BWAMEM:SAMTOOLS_INDEX' {
-        publishDir = [
-            [
-                path: { "${params.outdir}/${params.aligner}/deduplicated/" },
-                mode: params.publish_dir_mode,
-                pattern: "*.bai",
-                enabled: !params.skip_deduplication
-            ]
-        ]
-    }
 }

modules.json

@@ -95,6 +95,29 @@
                         "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
                         "installed_by": ["modules"]
                     },
+                    "parabricks/fq2bam": {
+                        "branch": "master",
+                        "git_sha": "1e4345f4e18eca1985e35562e8f5d29caf7f8206",
+                        "installed_by": [
+                            "_",
+                            "a",
+                            "b",
+                            "d",
+                            "e",
+                            "f",
+                            "g",
+                            "i",
+                            "l",
+                            "m",
+                            "n",
+                            "p",
+                            "q",
+                            "s",
+                            "t",
+                            "u",
+                            "w"
+                        ]
+                    },
                     "parabricks/fq2bammeth": {
                         "branch": "master",
                         "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
@@ -221,7 +244,26 @@
                     "bam_sort_stats_samtools": {
                         "branch": "master",
                         "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
-                        "installed_by": ["fastq_align_bwa"]
+                        "installed_by": [
+                            "_",
+                            "a",
+                            "b",
+                            "d",
+                            "e",
+                            "f",
+                            "fastq_align_bwa",
+                            "g",
+                            "i",
+                            "l",
+                            "m",
+                            "n",
+                            "p",
+                            "q",
+                            "s",
+                            "t",
+                            "u",
+                            "w"
+                        ]
                     },
                     "bam_stats_samtools": {
                         "branch": "master",
@@ -255,7 +297,7 @@
                     },
                     "fastq_align_dedup_bwamem": {
                         "branch": "master",
-                        "git_sha": "654daca6c7d8a17479d1c56fb5fb8d1663f11428",
+                        "git_sha": "e3d2496d0e47f444e6cd2cfddc9299ceb320c80e",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_align_dedup_bwameth": {