Merge pull request #358 from bjlang/dev

Dev
nf-core · Oct 16, 2023 · f9d6e65 · f9d6e65
2 parents f7d76c9 + fa3221e
commit f9d6e65
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Showing 17 changed files with 100 additions and 95 deletions.
diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
@@ -59,96 +59,99 @@ def check_samplesheet(file_in, file_out):
 
         ## Check sample entries
         for line in fin:
-            lspl = [x.strip().strip('"') for x in line.strip().split(",")]
-
-            # Check valid number of columns per row
-            if len(lspl) < len(HEADER):
-                print_error(
-                    "Invalid number of columns (minimum = {})!".format(len(HEADER)),
-                    "Line",
-                    line,
-                )
-            num_cols = len([x for x in lspl if x])
-            if num_cols < MIN_COLS:
-                print_error(
-                    "Invalid number of populated columns (minimum = {})!".format(MIN_COLS),
-                    "Line",
-                    line,
-                )
-
-            ## Check sample name entries
-            sample, fastq_1, fastq_2, replicate, antibody, control, control_replicate = lspl[: len(HEADER)]
-            if sample.find(" ") != -1:
-                print(f"WARNING: Spaces have been replaced by underscores for sample: {sample}")
-                sample = sample.replace(" ", "_")
-            if not sample:
-                print_error("Sample entry has not been specified!", "Line", line)
-
-            ## Check FastQ file extension
-            for fastq in [fastq_1, fastq_2]:
-                if fastq:
-                    if fastq.find(" ") != -1:
-                        print_error("FastQ file contains spaces!", "Line", line)
-                    if not fastq.endswith(".fastq.gz") and not fastq.endswith(".fq.gz"):
-                        print_error(
-                            "FastQ file does not have extension '.fastq.gz' or '.fq.gz'!",
-                            "Line",
-                            line,
-                        )
+            if line.strip():
+                lspl = [x.strip().strip('"') for x in line.strip().split(",")]
 
-            ## Check replicate column is integer
-            if not replicate.isdecimal():
-                print_error("Replicate id not an integer!", "Line", line)
-                sys.exit(1)
-
-            ## Check antibody and control columns have valid values
-            if antibody:
-                if antibody.find(" ") != -1:
-                    print(f"WARNING: Spaces have been replaced by underscores for antibody: {antibody}")
-                    antibody = antibody.replace(" ", "_")
-                if not control:
+                # Check valid number of columns per row
+                if len(lspl) < len(HEADER):
                     print_error(
-                        "Both antibody and control columns must be specified!",
+                        "Invalid number of columns (minimum = {})!".format(len(HEADER)),
                         "Line",
                         line,
                     )
-
-            if control:
-                if control.find(" ") != -1:
-                    print(f"WARNING: Spaces have been replaced by underscores for control: {control}")
-                    control = control.replace(" ", "_")
-                if not control_replicate.isdecimal():
-                    print_error("Control replicate id not an integer!", "Line", line)
-                    sys.exit(1)
-                control = "{}_REP{}".format(control, control_replicate)
-                if not antibody:
+                num_cols = len([x for x in lspl[: len(HEADER)] if x])
+                if num_cols < MIN_COLS:
                     print_error(
-                        "Both antibody and control columns must be specified!",
+                        "Invalid number of populated columns (minimum = {})!".format(MIN_COLS),
                         "Line",
                         line,
                     )
 
-            ## Auto-detect paired-end/single-end
-            sample_info = []  ## [single_end, fastq_1, fastq_2, replicate, antibody, control]
-            if sample and fastq_1 and fastq_2:  ## Paired-end short reads
-                sample_info = ["0", fastq_1, fastq_2, replicate, antibody, control]
-            elif sample and fastq_1 and not fastq_2:  ## Single-end short reads
-                sample_info = ["1", fastq_1, fastq_2, replicate, antibody, control]
-            else:
-                print_error("Invalid combination of columns provided!", "Line", line)
-
-            ## Create sample mapping dictionary = {sample: [[ single_end, fastq_1, fastq_2, replicate, antibody, control ]]}
-            replicate = int(replicate)
-            sample_info = sample_info + lspl[len(HEADER) :]
-            if sample not in sample_mapping_dict:
-                sample_mapping_dict[sample] = {}
-            if replicate not in sample_mapping_dict[sample]:
-                sample_mapping_dict[sample][replicate] = [sample_info]
-            else:
-                if sample_info in sample_mapping_dict[sample][replicate]:
-                    print_error("Samplesheet contains duplicate rows!", "Line", line)
+                ## Check sample name entries
+                sample, fastq_1, fastq_2, replicate, antibody, control, control_replicate = lspl[: len(HEADER)]
+                if sample.find(" ") != -1:
+                    print(f"WARNING: Spaces have been replaced by underscores for sample: {sample}")
+                    sample = sample.replace(" ", "_")
+                if not sample:
+                    print_error("Sample entry has not been specified!", "Line", line)
+
+                ## Check FastQ file extension
+                for fastq in [fastq_1, fastq_2]:
+                    if fastq:
+                        if fastq.find(" ") != -1:
+                            print_error("FastQ file contains spaces!", "Line", line)
+                        if not fastq.endswith(".fastq.gz") and not fastq.endswith(".fq.gz"):
+                            print_error(
+                                "FastQ file does not have extension '.fastq.gz' or '.fq.gz'!",
+                                "Line",
+                                line,
+                            )
+
+                ## Check replicate column is integer
+                if not replicate.isdecimal():
+                    print_error("Replicate id not an integer!", "Line", line)
+                    sys.exit(1)
+
+                ## Check antibody and control columns have valid values
+                if antibody:
+                    if antibody.find(" ") != -1:
+                        print(f"WARNING: Spaces have been replaced by underscores for antibody: {antibody}")
+                        antibody = antibody.replace(" ", "_")
+                    if not control:
+                        print_error(
+                            "Both antibody and control columns must be specified!",
+                            "Line",
+                            line,
+                        )
+
+                if control:
+                    if control.find(" ") != -1:
+                        print(f"WARNING: Spaces have been replaced by underscores for control: {control}")
+                        control = control.replace(" ", "_")
+                    if not control_replicate.isdecimal():
+                        print_error("Control replicate id not an integer!", "Line", line)
+                        sys.exit(1)
+                    control = "{}_REP{}".format(control, control_replicate)
+                    if not antibody:
+                        print_error(
+                            "Both antibody and control columns must be specified!",
+                            "Line",
+                            line,
+                        )
+
+                ## Auto-detect paired-end/single-end
+                sample_info = []  ## [single_end, fastq_1, fastq_2, replicate, antibody, control]
+                ## Paired-end short reads
+                if sample and fastq_1 and fastq_2:
+                    sample_info = ["0", fastq_1, fastq_2, replicate, antibody, control]
+                ## Single-end short reads
+                elif sample and fastq_1 and not fastq_2:
+                    sample_info = ["1", fastq_1, fastq_2, replicate, antibody, control]
+                else:
+                    print_error("Invalid combination of columns provided!", "Line", line)
+
+                ## Create sample mapping dictionary = {sample: [[ single_end, fastq_1, fastq_2, replicate, antibody, control ]]}
+                replicate = int(replicate)
+                sample_info = sample_info + lspl[len(HEADER) :]
+                if sample not in sample_mapping_dict:
+                    sample_mapping_dict[sample] = {}
+                if replicate not in sample_mapping_dict[sample]:
+                    sample_mapping_dict[sample][replicate] = [sample_info]
                 else:
-                    sample_mapping_dict[sample][replicate].append(sample_info)
+                    if sample_info in sample_mapping_dict[sample][replicate]:
+                        print_error("Samplesheet contains duplicate rows!", "Line", line)
+                    else:
+                        sample_mapping_dict[sample][replicate].append(sample_info)
 
     ## Write validated samplesheet with appropriate columns
     if len(sample_mapping_dict) > 0:

diff --git a/modules/local/bam_remove_orphans.nf b/modules/local/bam_remove_orphans.nf
@@ -8,7 +8,7 @@ process BAM_REMOVE_ORPHANS {
     conda "bioconda::pysam=0.19.0 bioconda::samtools=1.15.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-57736af1eb98c01010848572c9fec9fff6ffaafd:402e865b8f6af2f3e58c6fc8d57127ff0144b2c7-0' :
-        'quay.io/biocontainers/mulled-v2-57736af1eb98c01010848572c9fec9fff6ffaafd:402e865b8f6af2f3e58c6fc8d57127ff0144b2c7-0' }"
+        'biocontainers/mulled-v2-57736af1eb98c01010848572c9fec9fff6ffaafd:402e865b8f6af2f3e58c6fc8d57127ff0144b2c7-0' }"
 
     input:
     tuple val(meta), path(bam)

diff --git a/modules/local/bamtools_filter.nf b/modules/local/bamtools_filter.nf
@@ -5,7 +5,7 @@ process BAMTOOLS_FILTER {
     conda "bioconda::bamtools=2.5.2 bioconda::samtools=1.15.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-0560a8046fc82aa4338588eca29ff18edab2c5aa:5687a7da26983502d0a8a9a6b05ed727c740ddc4-0' :
-        'quay.io/biocontainers/mulled-v2-0560a8046fc82aa4338588eca29ff18edab2c5aa:5687a7da26983502d0a8a9a6b05ed727c740ddc4-0' }"
+        'biocontainers/mulled-v2-0560a8046fc82aa4338588eca29ff18edab2c5aa:5687a7da26983502d0a8a9a6b05ed727c740ddc4-0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)

diff --git a/modules/local/bedtools_genomecov.nf b/modules/local/bedtools_genomecov.nf
@@ -5,7 +5,7 @@ process BEDTOOLS_GENOMECOV {
     conda "bioconda::bedtools=2.30.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0':
-        'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
+        'biocontainers/bedtools:2.30.0--hc088bd4_0' }"
 
     input:
     tuple val(meta), path(bam), path(flagstat)

diff --git a/modules/local/deseq2_qc.nf b/modules/local/deseq2_qc.nf
@@ -7,7 +7,7 @@ process DESEQ2_QC {
     conda "conda-forge::r-base bioconda::bioconductor-deseq2 bioconda::bioconductor-biocparallel bioconda::bioconductor-tximport bioconda::bioconductor-complexheatmap conda-forge::r-optparse conda-forge::r-ggplot2 conda-forge::r-rcolorbrewer conda-forge::r-pheatmap"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0' :
-        'quay.io/biocontainers/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0' }"
+        'biocontainers/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0' }"
 
     input:
     tuple val(meta), path(counts)

diff --git a/modules/local/frip_score.nf b/modules/local/frip_score.nf
@@ -5,7 +5,7 @@ process FRIP_SCORE {
     conda "bioconda::bedtools=2.30.0 bioconda::samtools=1.15.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-8186960447c5cb2faa697666dc1e6d919ad23f3e:3127fcae6b6bdaf8181e21a26ae61231030a9fcb-0':
-        'quay.io/biocontainers/mulled-v2-8186960447c5cb2faa697666dc1e6d919ad23f3e:3127fcae6b6bdaf8181e21a26ae61231030a9fcb-0' }"
+        'biocontainers/mulled-v2-8186960447c5cb2faa697666dc1e6d919ad23f3e:3127fcae6b6bdaf8181e21a26ae61231030a9fcb-0' }"
 
     input:
     tuple val(meta), path(bam), path(peak)

diff --git a/modules/local/genome_blacklist_regions.nf b/modules/local/genome_blacklist_regions.nf
@@ -7,7 +7,7 @@ process GENOME_BLACKLIST_REGIONS {
     conda "bioconda::bedtools=2.30.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0':
-        'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
+        'biocontainers/bedtools:2.30.0--hc088bd4_0' }"
 
     input:
     path sizes

diff --git a/modules/local/gtf2bed.nf b/modules/local/gtf2bed.nf
@@ -5,7 +5,7 @@ process GTF2BED {
     conda "conda-forge::perl=5.26.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/perl:5.26.2':
-        'quay.io/biocontainers/perl:5.26.2' }"
+        'biocontainers/perl:5.26.2' }"
 
     input:
     path gtf

diff --git a/modules/local/igv.nf b/modules/local/igv.nf
@@ -6,7 +6,7 @@ process IGV {
     conda "conda-forge::python=3.8.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.8.3':
-        'quay.io/biocontainers/python:3.8.3' }"
+        'biocontainers/python:3.8.3' }"
 
     input:
     val aligner_dir

diff --git a/modules/local/macs2_consensus.nf b/modules/local/macs2_consensus.nf
@@ -8,7 +8,7 @@ process MACS2_CONSENSUS {
     conda "conda-forge::biopython conda-forge::r-optparse=1.7.1 conda-forge::r-upsetr=1.4.0 bioconda::bedtools=2.30.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-2f48cc59b03027e31ead6d383fe1b8057785dd24:5d182f583f4696f4c4d9f3be93052811b383341f-0':
-        'quay.io/biocontainers/mulled-v2-2f48cc59b03027e31ead6d383fe1b8057785dd24:5d182f583f4696f4c4d9f3be93052811b383341f-0' }"
+        'biocontainers/mulled-v2-2f48cc59b03027e31ead6d383fe1b8057785dd24:5d182f583f4696f4c4d9f3be93052811b383341f-0' }"
 
     input:
     tuple val(meta), path(peaks)

diff --git a/modules/local/multiqc.nf b/modules/local/multiqc.nf
@@ -4,7 +4,7 @@ process MULTIQC {
     conda "bioconda::multiqc=1.13a"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/multiqc:1.13a--pyhdfd78af_1':
-        'quay.io/biocontainers/multiqc:1.13a--pyhdfd78af_1' }"
+        'biocontainers/multiqc:1.13a--pyhdfd78af_1' }"
 
     input:
     path multiqc_config

diff --git a/modules/local/multiqc_custom_peaks.nf b/modules/local/multiqc_custom_peaks.nf
@@ -1,9 +1,10 @@
 process MULTIQC_CUSTOM_PEAKS {
     tag "$meta.id"
+
     conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'docker.io/library/ubuntu:20.04' }"
+        'nf-core/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(peak), path(frip)
@@ -13,6 +14,7 @@ process MULTIQC_CUSTOM_PEAKS {
     output:
     tuple val(meta), path("*.peak_count_mqc.tsv"), emit: count
     tuple val(meta), path("*.FRiP_mqc.tsv")      , emit: frip
+    path "versions.yml"                          , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/modules/local/multiqc_custom_phantompeakqualtools.nf b/modules/local/multiqc_custom_phantompeakqualtools.nf
@@ -3,7 +3,7 @@ process MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS {
     conda "conda-forge::r-base=3.5.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/r-base:3.5.1':
-        'quay.io/biocontainers/r-base:3.5.1' }"
+        'biocontainers/r-base:3.5.1' }"
 
     input:
     tuple val(meta), path(spp), path(rdata)

diff --git a/modules/local/plot_homer_annotatepeaks.nf b/modules/local/plot_homer_annotatepeaks.nf
@@ -4,7 +4,7 @@ process PLOT_HOMER_ANNOTATEPEAKS {
     conda "conda-forge::r-base=4.0.3 conda-forge::r-reshape2=1.4.4 conda-forge::r-optparse=1.6.6 conda-forge::r-ggplot2=3.3.3 conda-forge::r-scales=1.1.1 conda-forge::r-viridis=0.5.1 conda-forge::r-tidyverse=1.3.0 bioconda::bioconductor-biostrings=2.58.0 bioconda::bioconductor-complexheatmap=2.6.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-ad9dd5f398966bf899ae05f8e7c54d0fb10cdfa7:05678da05b8e5a7a5130e90a9f9a6c585b965afa-0':
-        'quay.io/biocontainers/mulled-v2-ad9dd5f398966bf899ae05f8e7c54d0fb10cdfa7:05678da05b8e5a7a5130e90a9f9a6c585b965afa-0' }"
+        'biocontainers/mulled-v2-ad9dd5f398966bf899ae05f8e7c54d0fb10cdfa7:05678da05b8e5a7a5130e90a9f9a6c585b965afa-0' }"
 
     input:
     path annos

diff --git a/modules/local/plot_macs2_qc.nf b/modules/local/plot_macs2_qc.nf
@@ -4,7 +4,7 @@ process PLOT_MACS2_QC {
     conda "conda-forge::r-base=4.0.3 conda-forge::r-reshape2=1.4.4 conda-forge::r-optparse=1.6.6 conda-forge::r-ggplot2=3.3.3 conda-forge::r-scales=1.1.1 conda-forge::r-viridis=0.5.1 conda-forge::r-tidyverse=1.3.0 bioconda::bioconductor-biostrings=2.58.0 bioconda::bioconductor-complexheatmap=2.6.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-ad9dd5f398966bf899ae05f8e7c54d0fb10cdfa7:05678da05b8e5a7a5130e90a9f9a6c585b965afa-0':
-        'quay.io/biocontainers/mulled-v2-ad9dd5f398966bf899ae05f8e7c54d0fb10cdfa7:05678da05b8e5a7a5130e90a9f9a6c585b965afa-0' }"
+        'biocontainers/mulled-v2-ad9dd5f398966bf899ae05f8e7c54d0fb10cdfa7:05678da05b8e5a7a5130e90a9f9a6c585b965afa-0' }"
 
     input:
     path peaks

diff --git a/modules/local/star_align.nf b/modules/local/star_align.nf
@@ -6,7 +6,7 @@ process STAR_ALIGN {
     conda "bioconda::star=2.6.1d"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/star:2.6.1d--0' :
-        'quay.io/biocontainers/star:2.6.1d--0' }"
+        'biocontainers/star:2.6.1d--0' }"
 
     input:
     tuple val(meta) , path(reads)

diff --git a/modules/local/star_genomegenerate.nf b/modules/local/star_genomegenerate.nf
@@ -6,7 +6,7 @@ process STAR_GENOMEGENERATE {
     conda "bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' :
-        'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }"
+        'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }"
 
     input:
     path fasta