Chore/bump modules

.nf-core.yml

@@ -38,5 +38,5 @@ template:
   name: preprocessing
   org: nf-cmgg
   outdir: .
-  skip_features: []
+  skip_features: ["fastqc"]
   version: 2.1.0dev

README.md

@@ -23,7 +23,7 @@ Steps inlcude:
 
 1. Demultiplexing using [`BCLconvert`](https://emea.support.illumina.com/sequencing/sequencing_software/bcl-convert.html)
 2. Read QC and trimming using [`fastp`](https://github.com/OpenGene/fastp)
-3. Alignment using either [`bwa`](https://github.com/lh3/bwa), [`bwa-mem2`](https://github.com/bwa-mem2/bwa-mem2), [`bowtie2`](https://github.com/BenLangmead/bowtie2), [`dragmap`](https://github.com/Illumina/DRAGMAP) or [`snap`](https://github.com/amplab/snap) for DNA-seq and [`STAR`](https://github.com/alexdobin/STAR) for RNA-seq
+3. Alignment using either [`bwa`](https://github.com/lh3/bwa), [`bwa-mem2`](https://github.com/bwa-mem2/bwa-mem2), [`bowtie2`](https://github.com/BenLangmead/bowtie2), [`dragmap`](https://github.com/Illumina/DRAGMAP), [`snap`](https://github.com/amplab/snap) or [`strobe`](https://github.com/ksahlin/strobealign) for DNA-seq and [`STAR`](https://github.com/alexdobin/STAR) for RNA-seq
 4. Duplicate marking using [`bamsormadup`](https://gitlab.com/german.tischler/biobambam2) or [`samtools markdup`](http://www.htslib.org/doc/samtools-markdup.html)
 5. Coverage analysis using [`mosdepth`](https://github.com/brentp/mosdepth) and [`samtools coverage`](http://www.htslib.org/doc/samtools-coverage.html)
 6. Alignment QC using [`samtools flagstat`](http://www.htslib.org/doc/samtools-flagstat.html), [`samtools stats`](http://www.htslib.org/doc/samtools-stats.html), [`samtools idxstats`](http://www.htslib.org/doc/samtools-idxstats.html) and [`picard CollecHsMetrics`](https://broadinstitute.github.io/picard/command-line-overview.html#CollectHsMetrics), [`picard CollectWgsMetrics`](https://broadinstitute.github.io/picard/command-line-overview.html#CollectWgsMetrics), [`picard CollectMultipleMetrics`](https://broadinstitute.github.io/picard/command-line-overview.html#CollectMultipleMetrics)

assets/schema_input.json

@@ -37,7 +37,7 @@
                 "meta": ["aligner"],
                 "type": "string",
                 "description": "Aligner to use to align sample to the reference genome",
-                "enum": ["bowtie2", "bwamem", "bwamem2", "dragmap", "snap", "star"]
+                "enum": ["bowtie2", "bwamem", "bwamem2", "dragmap", "snap", "strobe", "star"]
             },
             "tag": {
                 "meta": ["tag"],

assets/schema_sampleinfo.json

@@ -85,7 +85,7 @@
                 "meta": ["aligner"],
                 "type": "string",
                 "description": "Aligner to use to align sample to the reference genome",
-                "enum": ["bowtie2", "bwamem", "bwamem2", "dragmap", "snap", "star"]
+                "enum": ["bowtie2", "bwamem", "bwamem2", "dragmap", "snap", "strobe", "star"]
             }
         }
     },

conf/modules.config

@@ -21,7 +21,7 @@ process {
             [
                 meta.lane ? "--bcl-only-lane ${meta.lane}" : "",
                 "--force",
-                "--strict",
+                "--strict-mode true",
             ].join(" ").trim()
         }
     }
@@ -49,7 +49,7 @@ process {
         ext.args   = {
             [
                 meta.readgroup ? "--rg-line \"@RG\t" + meta.readgroup.findResults { rg -> rg.value?.trim() ? "${rg.key}:${rg.value}" : null }.join("\t") + "\"" : "",
-                "--output-fmt cram",
+                "--output-fmt cram,version=3.0",
                 "--output-fmt-option archive",
             ].join(" ").trim()
         }
@@ -113,7 +113,7 @@ process {
     // -xf 2  : expansion factor for reading compressed data
 
     //// SNAP
-    withName: SNAP_ALIGN {
+    withName: SNAPALIGNER_ALIGN {
         ext.args = {
             [
                 "-b-",
@@ -154,7 +154,7 @@ process {
                 "-d 2500",
                 params.umi_aware ? "--barcode-name" : "",
                 "--write-index",
-                "--output-fmt cram",
+                "--output-fmt cram,version=3.0",
                 "--output-fmt-option archive",
             ].join(" ").trim()
         }
@@ -166,7 +166,7 @@ process {
         ext.args   = {
             [
                 "--write-index",
-                "--output-fmt cram",
+                "--output-fmt cram,version=3.0",
                 "--output-fmt-option archive",
             ].join(" ").trim()
         }
@@ -191,7 +191,7 @@ process {
         ext.args   = {
             [
                 "-C",
-                "--output-fmt cram",
+                "--output-fmt cram,version=3.0",
                 "--output-fmt-option archive",
             ].join(" ").trim()
         }

conf/profiles/s3_ugent.config

@@ -1,4 +1,5 @@
 aws {
+    profile = "ugent"
     client {
         endpoint          = "https://s3.ugent.be"
         protocol          = "https"

main.nf

@@ -66,8 +66,8 @@ workflow {
 
     publish:
     demultiplex_interop = PREPROCESSING.out.demultiplex_interop.transpose(by:1)
-    demultiplex_reports = PREPROCESSING.out.demultiplex_reports.map { meta, reports -> [ meta, files("${reports.toUri()}/*") ] }.transpose(by:1)
-    demultiplex_logs    = PREPROCESSING.out.demultiplex_logs.map { meta, logs -> [ meta, files("${logs.toUri()}/*") ] }.transpose(by:1)
+    demultiplex_reports = PREPROCESSING.out.demultiplex_reports.transpose(by:1)
+    demultiplex_logs    = PREPROCESSING.out.demultiplex_logs.transpose(by:1)
     fastp_json          = PREPROCESSING.out.fastp_json
     fastp_html          = PREPROCESSING.out.fastp_html
     ucrams              = PREPROCESSING.out.ucrams
@@ -107,11 +107,11 @@ output {
         bin >> "Interop/${bin.name}"
     } }
     demultiplex_reports { path { meta, report ->
-        def out_path = meta.lane ? "Reports/LOO${meta.lane}/${report.name}" as String : "Reports/${report.name}"
+        def out_path = meta.lane ? "Reports/L00${meta.lane}/${report.name}" as String : "Reports/${report.name}"
         report >> out_path
     } }
     demultiplex_logs { path { meta, log ->
-        def out_path = meta.lane ? "Logs/LOO${meta.lane}/${log.name}" as String : "Logs/${log.name}"
+        def out_path = meta.lane ? "Logs/L00${meta.lane}/${log.name}" as String : "Logs/${log.name}"
         log >> out_path
     } }
     fastp_json { path { meta, json ->

modules.json

@@ -7,143 +7,138 @@
                 "nf-core": {
                     "bcl2fastq": {
                         "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["bcl_demultiplex"]
                     },
                     "bclconvert": {
                         "branch": "master",
-                        "git_sha": "27cceb2eb8aa959d4a8819caab886386a59a3789",
-                        "installed_by": ["bcl_demultiplex", "modules"]
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
+                        "installed_by": ["bcl_demultiplex", "modules"],
+                        "patch": "modules/nf-core/bclconvert/bclconvert.diff"
                     },
                     "biobambam/bamsormadup": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/biobambam/bamsormadup/biobambam-bamsormadup.diff"
                     },
                     "bowtie2/align": {
                         "branch": "master",
-                        "git_sha": "8864afe586537bf562eac7b83349c26207f3cb4d",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["fastq_align_dna", "modules"],
                         "patch": "modules/nf-core/bowtie2/align/bowtie2-align.diff"
                     },
                     "bwa/mem": {
                         "branch": "master",
-                        "git_sha": "a29f18660f5e3748d44d6f716241e70c942c065d",
+                        "git_sha": "1c46359c837ef768b004519f535c30378e8289fc",
                         "installed_by": ["fastq_align_dna"],
                         "patch": "modules/nf-core/bwa/mem/bwa-mem.diff"
                     },
                     "bwamem2/mem": {
                         "branch": "master",
-                        "git_sha": "a29f18660f5e3748d44d6f716241e70c942c065d",
+                        "git_sha": "d86336f3e7ae0d5f76c67b0859409769cfeb2af2",
                         "installed_by": ["fastq_align_dna"],
                         "patch": "modules/nf-core/bwamem2/mem/bwamem2-mem.diff"
                     },
                     "dragmap/align": {
                         "branch": "master",
-                        "git_sha": "8864afe586537bf562eac7b83349c26207f3cb4d",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["fastq_align_dna"],
                         "patch": "modules/nf-core/dragmap/align/dragmap-align.diff"
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/fastp/fastp.diff"
-                    },
-                    "fastqc": {
-                        "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "d9ec4ef289ad39b8a662a7a12be50409b11df84b",
                         "installed_by": ["modules"]
                     },
                     "md5sum": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["modules"]
                     },
                     "mosdepth": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/mosdepth/mosdepth.diff"
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "471cf3ca1617271b9b6fea09ea2ebdee78b874de",
+                        "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
                         "installed_by": ["modules"]
                     },
                     "picard/collecthsmetrics": {
                         "branch": "master",
-                        "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/picard/collecthsmetrics/picard-collecthsmetrics.diff"
                     },
                     "picard/collectmultiplemetrics": {
                         "branch": "master",
-                        "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
+                        "git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/picard/collectmultiplemetrics/picard-collectmultiplemetrics.diff"
                     },
                     "picard/collectwgsmetrics": {
                         "branch": "master",
-                        "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
+                        "git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/picard/collectwgsmetrics/picard-collectwgsmetrics.diff"
                     },
                     "samtools/cat": {
                         "branch": "master",
-                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
+                        "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/samtools/cat/samtools-cat.diff"
                     },
                     "samtools/convert": {
                         "branch": "master",
-                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/samtools/convert/samtools-convert.diff"
                     },
                     "samtools/coverage": {
                         "branch": "master",
-                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/samtools/coverage/samtools-coverage.diff"
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
+                        "git_sha": "e334e12a1e985adc5ffc3fc78a68be1de711de45",
                         "installed_by": ["modules"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
+                        "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
                         "installed_by": ["modules"]
                     },
                     "samtools/import": {
                         "branch": "master",
-                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
+                        "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
                         "installed_by": ["modules"]
                     },
                     "samtools/sormadup": {
                         "branch": "master",
-                        "git_sha": "38f3b0200093498b70ac2d63a83eac5642e3c873",
+                        "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/samtools/sormadup/samtools-sormadup.diff"
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b",
+                        "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/samtools/sort/samtools-sort.diff"
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
+                        "git_sha": "0b2435805036a16dcdcf21533632d956b8273ac4",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/samtools/stats/samtools-stats.diff"
                     },
                     "snapaligner/align": {
                         "branch": "master",
-                        "git_sha": "77bdd7e1047d2abe21ae8d89acc295ea553ecbae",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["fastq_align_dna", "modules"],
                         "patch": "modules/nf-core/snapaligner/align/snapaligner-align.diff"
                     },
@@ -152,21 +147,26 @@
                         "git_sha": "ce9e10540a1555145ddd1ddd8b15f7443cbe1449",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/star/align/star-align.diff"
+                    },
+                    "strobealign": {
+                        "branch": "master",
+                        "git_sha": "d5cc72b63c4e1565cb66e83f0577b04c0bb54d5c",
+                        "installed_by": ["fastq_align_dna", "modules"],
+                        "patch": "modules/nf-core/strobealign/strobealign.diff"
                     }
                 }
             },
             "subworkflows": {
                 "nf-core": {
                     "bcl_demultiplex": {
                         "branch": "master",
-                        "git_sha": "1a0770da1cf5c5cd388bf888ba8798bc4d1fba56",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_align_dna": {
                         "branch": "master",
-                        "git_sha": "a29f18660f5e3748d44d6f716241e70c942c065d",
-                        "installed_by": ["subworkflows"],
-                        "patch": "subworkflows/nf-core/fastq_align_dna/fastq_align_dna.diff"
+                        "git_sha": "070ddae7fb59384d3d85bf69eb9a1d71ab33ada9",
+                        "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
@@ -175,7 +175,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2",
+                        "git_sha": "df4d1c8cdee98a1bbbed8fc51e82296568e0f9c1",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {