update all modules + subworkflows / remove tags + path markduplicates

Author: maxulysse

modules.json

@@ -47,7 +47,7 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"]
                     },
                     "fq/subsample": {
@@ -97,7 +97,7 @@
                     },
                     "picard/markduplicates": {
                         "branch": "master",
-                        "git_sha": "0dee12b56ccecc416d6f7a1ccd85fd571eab3307",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["bam_markduplicates_picard"],
                         "patch": "modules/nf-core/picard/markduplicates/picard-markduplicates.diff"
                     },
@@ -108,7 +108,7 @@
                     },
                     "qualimap/rnaseq": {
                         "branch": "master",
-                        "git_sha": "6b0e4fe14ca1b12e131f64608f0bbaf36fd11451",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["modules"]
                     },
                     "rsem/calculateexpression": {
@@ -173,17 +173,17 @@
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": [
                             "bam_dedup_stats_samtools_umitools",
                             "bam_markduplicates_picard",
@@ -192,12 +192,12 @@
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["bam_sort_stats_samtools"]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "sortmerna": {
@@ -207,17 +207,17 @@
                     },
                     "star/align": {
                         "branch": "master",
-                        "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["modules"]
                     },
                     "star/genomegenerate": {
                         "branch": "master",
-                        "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["modules"]
                     },
                     "stringtie/stringtie": {
                         "branch": "master",
-                        "git_sha": "b1b959609bda44341120aed1766329909f54b8d0",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["modules"]
                     },
                     "subread/featurecounts": {
@@ -247,7 +247,7 @@
                     },
                     "ucsc/bedgraphtobigwig": {
                         "branch": "master",
-                        "git_sha": "7c75d01997236f61b9b77399d9933cb36041f2c3",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
                     },
                     "umitools/dedup": {
@@ -276,12 +276,12 @@
                 "nf-core": {
                     "bam_dedup_stats_samtools_umitools": {
                         "branch": "master",
-                        "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_markduplicates_picard": {
                         "branch": "master",
-                        "git_sha": "0dee12b56ccecc416d6f7a1ccd85fd571eab3307",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_rseqc": {
@@ -291,7 +291,7 @@
                     },
                     "bam_sort_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["fastq_align_hisat2"]
                     },
                     "bam_stats_samtools": {
@@ -315,12 +315,12 @@
                     },
                     "fastq_fastqc_umitools_fastp": {
                         "branch": "master",
-                        "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"]
                     },
                     "fastq_fastqc_umitools_trimgalore": {
                         "branch": "master",
-                        "git_sha": "f3aef88fcb3101e404b8385dbabaaba06f898dc4",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"]
                     },
                     "fastq_qc_trim_filter_setstrandedness": {