Finish preparations for chromHMM

nf-core · Mar 26, 2024 · 19a2dc0 · 19a2dc0
1 parent 814eb4a
commit 19a2dc0
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Showing 8 changed files with 203 additions and 12 deletions.
diff --git a/assets/schema_input_bam.json b/assets/schema_input_bam.json
@@ -7,6 +7,12 @@
     "items": {
         "type": "object",
         "properties": {
+            "sample": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "Sample name must be provided and cannot contain spaces",
+                "meta": ["id"]
+            },
             "condition": {
                 "type": "string",
                 "pattern": "^\\S+$",
@@ -34,6 +40,6 @@
                 "errorMessage": "Control file must be provided and must be a .bam file"
             }
         },
-        "required": ["condition", "antibody", "signal", "control"]
+        "required": ["sample", "condition", "antibody", "signal", "control"]
     }
 }
diff --git a/conf/modules.config b/conf/modules.config
@@ -54,6 +54,13 @@ process {
         ext.prefix = {"${meta.id}.merged"}
     }
 
+    withName: ".*:CHROMHMM:REHEADER.*" {
+        ext.args = "-c 'sed -e \"s/SN:\\([0-9XY]*\\)/SN:chr\\\\1/\" -e \"s/SN:MT/SN:chrM/\"'"
+    }
+
+    withName: ".*:CHROMHMM:REHEADER_CONTROL" {
+        ext.prefix = {"${meta.id}_control"}
+    }
     withName: ".*DYNAMITE:FILTER" {
         ext.args = {"'BEGIN{OFS=\"\\t\"} NR==1 || (\$2 >= ${params.dynamite_min_regression} || \$2 <= -${params.dynamite_min_regression} )'"}
         ext.prefix = {"${meta.id}.filtered"}

diff --git a/modules.json b/modules.json
@@ -8,37 +8,58 @@
                     "atlasgeneannotationmanipulation/gtf2featureannotation": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "bedtools/merge": {
                         "branch": "master",
                         "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "bedtools/sort": {
                         "branch": "master",
                         "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "bedtools/subtract": {
                         "branch": "master",
                         "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "cat/cat": {
                         "branch": "master",
                         "git_sha": "9437e6053dccf4aafa022bfd6e7e9de67e625af8",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "deseq2/differential": {
                         "branch": "master",
                         "git_sha": "9326d73af3fbe2ee90d9ce0a737461a727c5118e",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "gawk": {
                         "branch": "master",
                         "git_sha": "dc3527855e7358c6d8400828754c0caa5f11698f",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
+                    },
+                    "samtools/reheader": {
+                        "branch": "master",
+                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "installed_by": [
+                            "modules"
+                        ]
                     }
                 }
             },
@@ -47,20 +68,26 @@
                     "utils_nextflow_pipeline": {
                         "branch": "master",
                         "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
                         "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     },
                     "utils_nfvalidation_plugin": {
                         "branch": "master",
                         "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     }
                 }
             }
         }
     }
-}
+}
diff --git a/modules/nf-core/samtools/reheader/environment.yml b/modules/nf-core/samtools/reheader/environment.yml
diff --git a/modules/nf-core/samtools/reheader/main.nf b/modules/nf-core/samtools/reheader/main.nf
diff --git a/modules/nf-core/samtools/reheader/meta.yml b/modules/nf-core/samtools/reheader/meta.yml
diff --git a/subworkflows/local/chromhmm.nf b/subworkflows/local/chromhmm.nf
@@ -0,0 +1,41 @@
+// Modules
+include { SAMTOOLS_REHEADER as REHEADER_SIGNAL  } from '../../modules/nf-core/samtools/reheader'
+include { SAMTOOLS_REHEADER as REHEADER_CONTROL } from '../../modules/nf-core/samtools/reheader'
+
+workflow CHROMHMM {
+
+    take:
+    ch_samplesheet_bam
+
+    main:
+
+    ch_versions = Channel.empty()
+
+    ch_bams = ch_samplesheet_bam.map{meta, signal, control -> [meta, ["signal", "control"], [signal, control]]}
+                                .transpose()
+                                .map{meta, type, bam -> [meta + [type: type], bam]}
+                                .branch   {meta, bam -> 
+                                    control: meta.type == "control"
+                                    signal:  meta.type == "signal"
+                                }
+
+    def remove_type = {meta, bam -> [[  id: meta.id,
+                                        condition: meta.condition,
+                                        antibody: meta.antibody], 
+                                    bam]}
+
+    ch_signal  = REHEADER_SIGNAL (ch_bams.signal ).bam.map{meta, bam -> remove_type(meta, bam)}
+    ch_control = REHEADER_CONTROL(ch_bams.control).bam.map{meta, bam -> remove_type(meta, bam)}
+    ch_combined = ch_signal.join(ch_control)
+    ch_table = ch_combined  .map{meta, signal, control -> [meta.condition, meta.antibody, signal.name, control.name]}
+                            .collectFile() {
+                                ["cellmarktable.txt", it.join("\t") + "\n"]
+                            }
+    ch_table.view()
+
+
+    emit:
+
+    versions = ch_versions                     // channel: [ versions.yml ]
+}
+
diff --git a/subworkflows/local/peaks.nf b/subworkflows/local/peaks.nf
@@ -11,6 +11,7 @@ include { COMBINE_TABLES as AFFINITY_SUM  } from '../../modules/local/combine_ta
 // Subworkflows
 include { FOOTPRINTING               } from './footprinting'
 include { MERGE_SAMPLES              } from './merge_samples'
+include { CHROMHMM                   } from './chromhmm'
 
 workflow PEAKS {
 
@@ -56,6 +57,8 @@ workflow PEAKS {
         ch_versions = ch_versions.mix(SORT_PEAKS.out.versions)
     }
 
+    CHROMHMM(ch_samplesheet_bam)
+
     FILTER_PWMS(tfs, pwms)
 
     STARE(