nf-core · JoseEspinosa · Apr 17, 2023 · Apr 17, 2023 · Apr 17, 2023 · Apr 17, 2023
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Updated pipeline template to [nf-core/tools 2.7.2](https://github.com/nf-core/tools/releases/tag/2.7.2)
 - [[#317](https://github.com/nf-core/chipseq/issues/317)] Added metro map
+- [[#288](https://github.com/nf-core/chipseq/issues/291)] Bump `chromap` version 2 and enable all the steps below chromap again when paired-end data is processed.
 
 ## [[2.0.0](https://github.com/nf-core/chipseq/releases/tag/2.0.0)] - 2022-10-03
 

diff --git a/bin/bampe_rm_orphan.py b/bin/bampe_rm_orphan.py
@@ -46,7 +46,6 @@
 
 
 def makedir(path):
-
     if not len(path) == 0:
         try:
             os.makedirs(path)
@@ -63,7 +62,6 @@ def makedir(path):
 
 
 def bampe_rm_orphan(BAMIn, BAMOut, onlyFRPairs=False):
-
     ## SETUP DIRECTORY/FILE STRUCTURE
     OutDir = os.path.dirname(BAMOut)
     makedir(OutDir)
@@ -89,7 +87,6 @@ def bampe_rm_orphan(BAMIn, BAMOut, onlyFRPairs=False):
             ## FILTER FOR READS ON SAME CHROMOSOME IN FR ORIENTATION
             if onlyFRPairs:
                 if pair1.tid == pair2.tid:
-
                     ## READ1 FORWARD AND READ2 REVERSE STRAND
                     if not pair1.is_reverse and pair2.is_reverse:
                         if pair1.reference_start <= pair2.reference_start:

diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
@@ -49,7 +49,6 @@ def check_samplesheet(file_in, file_out):
 
     sample_mapping_dict = {}
     with open(file_in, "r", encoding="utf-8-sig") as fin:
-
         ## Check header
         MIN_COLS = 2
         HEADER = ["sample", "fastq_1", "fastq_2", "antibody", "control"]
@@ -156,7 +155,6 @@ def check_samplesheet(file_in, file_out):
                 + "\n"
             )
             for sample in sorted(sample_mapping_dict.keys()):
-
                 ## Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end
                 if not all(x[0] == sample_mapping_dict[sample][0][0] for x in sample_mapping_dict[sample]):
                     print_error(

diff --git a/bin/igv_files_to_session.py b/bin/igv_files_to_session.py
@@ -55,7 +55,6 @@
 
 
 def makedir(path):
-
     if not len(path) == 0:
         try:
             os.makedirs(path)
@@ -72,7 +71,6 @@ def makedir(path):
 
 
 def igv_files_to_session(XMLOut, ListFile, ReplaceFile, Genome, PathPrefix=""):
-
     makedir(os.path.dirname(XMLOut))
 
     replaceFileDict = {}

diff --git a/bin/macs2_merged_expand.py b/bin/macs2_merged_expand.py
@@ -55,7 +55,6 @@
 
 
 def makedir(path):
-
     if not len(path) == 0:
         try:
             os.makedirs(path)
@@ -78,7 +77,6 @@ def makedir(path):
 
 
 def macs2_merged_expand(MergedIntervalTxtFile, SampleNameList, OutFile, isNarrow=False, minReplicates=1):
-
     makedir(os.path.dirname(OutFile))
 
     combFreqDict = {}

diff --git a/modules.json b/modules.json
@@ -27,12 +27,12 @@
                     },
                     "chromap/chromap": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "d6b7b1f108dab88b0269a4331767c36a1a8da960",
                         "installed_by": ["modules"]
                     },
                     "chromap/index": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "d6b7b1f108dab88b0269a4331767c36a1a8da960",
                         "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {

diff --git a/modules/nf-core/chromap/chromap/main.nf b/modules/nf-core/chromap/chromap/main.nf
diff --git a/modules/nf-core/chromap/chromap/meta.yml b/modules/nf-core/chromap/chromap/meta.yml
diff --git a/modules/nf-core/chromap/index/main.nf b/modules/nf-core/chromap/index/main.nf
diff --git a/modules/nf-core/chromap/index/meta.yml b/modules/nf-core/chromap/index/meta.yml
diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf
@@ -176,10 +176,10 @@ workflow PREPARE_GENOME {
                 ch_chromap_index = UNTAR_CHROMAP_INDEX ( [ [:], params.chromap_index ] ).untar.map{ it[1] }
                 ch_versions  = ch_versions.mix(UNTAR.out.versions)
             } else {
-                ch_chromap_index = file(params.chromap_index)
+                ch_chromap_index = [ [:], file(params.chromap_index) ]
             }
         } else {
-            ch_chromap_index = CHROMAP_INDEX ( ch_fasta ).index
+            ch_chromap_index = CHROMAP_INDEX ( [ [:], ch_fasta ] ).index
             ch_versions  = ch_versions.mix(CHROMAP_INDEX.out.versions)
         }
     }

diff --git a/workflows/chipseq.nf b/workflows/chipseq.nf
@@ -208,39 +208,11 @@ workflow CHIPSEQ {
             FASTQC_TRIMGALORE.out.reads,
             PREPARE_GENOME.out.chromap_index,
             PREPARE_GENOME.out.fasta
+                .map {
+                    [ [:], it ]
+                }
         )
-
-        // Filter out paired-end reads until the issue below is fixed
-        // https://github.com/nf-core/chipseq/issues/291
-        // ch_genome_bam = ALIGN_CHROMAP.out.bam
-        ALIGN_CHROMAP
-            .out
-            .bam
-            .branch {
-                meta, bam ->
-                    single_end: meta.single_end
-                        return [ meta, bam ]
-                    paired_end: !meta.single_end
-                        return [ meta, bam ]
-            }
-            .set { ch_genome_bam_chromap }
-
-        ch_genome_bam_chromap
-            .paired_end
-            .collect()
-            .map {
-                it ->
-                    def count = it.size()
-                    if (count > 0) {
-                        log.warn "=============================================================================\n" +
-                        "  Paired-end files produced by chromap cannot be used by some downstream tools due to the issue below:\n" +
-                        "  https://github.com/nf-core/chipseq/issues/291\n" +
-                        "  They will be excluded from the analysis. Consider using a different aligner\n" +
-                        "==================================================================================="
-                    }
-            }
-
-        ch_genome_bam        = ch_genome_bam_chromap.single_end
+        ch_genome_bam        = ALIGN_CHROMAP.out.bam
         ch_genome_bam_index  = ALIGN_CHROMAP.out.bai
         ch_samtools_stats    = ALIGN_CHROMAP.out.stats
         ch_samtools_flagstat = ALIGN_CHROMAP.out.flagstat