Merge pull request #28 from sanger-tol/dp24_gc_content

Dp24 gc content

bin/gc_content.py

@@ -0,0 +1,33 @@
+#!/usr/bin/env python3
+"""
+Script for finding the GC content of each sequence in a multiFASTA file
+
+Written by Eerik Aunin @eeaunin
+
+Adapted by Damon-Lee Pointon @DLBPointon
+"""
+
+import argparse
+import general_purpose_functions as gpf
+
+
+def main(fasta_path):
+    fasta_data = gpf.read_fasta_in_chunks(fasta_path)
+    for header, seq in fasta_data:
+        header = header.split()[0]
+        seq = seq.upper()
+        gc_content = None
+        gc_count = seq.count("G") + seq.count("C")
+        seq_len = len(seq)
+        if seq_len > 0:
+            gc_content = gc_count / seq_len
+        gc_content_string = "{:.6f}".format(gc_content)
+        print("{}\t{}".format(header, gc_content_string))
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description=__doc__)
+    parser.add_argument("fasta_path", type=str, help="Path to input FASTA file")
+    parser.add_argument("-v", action="version", version="1.0")
+    args = parser.parse_args()
+    main(args.fasta_path)

bin/reformat_blast_outfmt6.py

@@ -23,20 +23,6 @@
 in_data = gpf.ll(in_path)
 
 for line in in_data:
-    split_line = line.split()
-    assert len(split_line) == 14
-    output_line = "{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}".format(
-        split_line[0],
-        split_line[4],
-        split_line[5],
-        split_line[6],
-        split_line[7],
-        split_line[8],
-        split_line[9],
-        split_line[10],
-        split_line[11],
-        split_line[12],
-        split_line[13],
-        split_line[2],
-    )
-    print(output_line)
+    s = line.split()
+    assert len(s) == 14
+    print("\t".join(s[0:1] + s[4:] + s[2:3]))

conf/modules.config

@@ -52,4 +52,9 @@ process {
         ext.prefix  = { "${meta.id}_euk" }
     }
 
+    withName: '.*:.*:GENERATE_GENOME:GNU_SORT' {
+        ext.prefix  = { "${meta.id}_sorted"}
+        ext.args    = { '-k2,2 -nr' }
+    }
+
 }

conf/test_full.config

@@ -9,6 +9,13 @@
 
 ----------------------------------------------------------------------------------------
 */
+process {
+    maxForks = 1
+}
+
+executor {
+    queueSize=1
+}
 
 params {
     config_profile_name        = 'Full test profile'

modules.json

@@ -20,6 +20,12 @@
                         "git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543",
                         "installed_by": ["modules"]
                     },
+                    "custom/getchromsizes": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/custom/getchromsizes/custom-getchromsizes.diff"
+                    },
                     "diamond/blastx": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
@@ -35,6 +41,11 @@
                         "git_sha": "5a35af8b60d45425c4b9193e567d16b614d93dbe",
                         "installed_by": ["modules"]
                     },
+                    "gnu/sort": {
+                        "branch": "master",
+                        "git_sha": "88f6e982fb8bd40488d837b3b08a65008e602840",
+                        "installed_by": ["modules"]
+                    },
                     "fcs/fcsgx": {
                         "branch": "master",
                         "git_sha": "8c4542e5d421c4690cf1fa6ec729e9304763fdaf",
@@ -66,6 +77,11 @@
                         "git_sha": "a1ffbc1fd87bd5a829e956cc26ec9cc53af3e817",
                         "installed_by": ["modules"]
                     },
+                    "samtools/faidx": {
+                        "branch": "master",
+                        "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe",
+                        "installed_by": ["modules"]
+                    },
                     "samtools/index": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",

modules/local/blast_chunk_to_full.nf

@@ -2,10 +2,10 @@ process BLAST_CHUNK_TO_FULL {
     tag "${meta.id}"
     label 'process_low'
 
-    conda "conda-forge::python=3.9 conda-forge::pandas=1.5.2"
+    conda "conda-forge::python=3.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pandas:1.5.2' :
-        'quay.io/biocontainers/pandas:1.5.2' }"
+        'https://depot.galaxyproject.org/singularity/python:3.9' :
+        'biocontainers/python:3.9' }"
 
     input:
     tuple val(meta), path(chunked)
@@ -22,6 +22,7 @@ process BLAST_CHUNK_TO_FULL {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
         blast_hit_chunk_coords_to_full_coords: \$(blast_hit_chunk_coords_to_full_coords.py -v)
     END_VERSIONS
     """

modules/local/blast_get_top_hits.nf

@@ -2,10 +2,10 @@ process BLAST_GET_TOP_HITS {
     tag "${meta.id}"
     label 'process_low'
 
-    conda "conda-forge::python=3.9 conda-forge::pandas=1.5.2"
+    conda "conda-forge::python=3.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pandas:1.5.2' :
-        'quay.io/biocontainers/pandas:1.5.2' }"
+        'https://depot.galaxyproject.org/singularity/python:3.9' :
+        'biocontainers/python:3.9' }"
 
     input:
     tuple val(meta), path(outfmt6)
@@ -21,6 +21,7 @@ process BLAST_GET_TOP_HITS {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
         blast_get_top_hits: \$(blast_get_top_hits.py -v)
     END_VERSIONS
     """
@@ -31,6 +32,7 @@ process BLAST_GET_TOP_HITS {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
         reformat_blast_outfmt6: \$(blast_get_top_hits.py -v)
     END_VERSIONS
     """

modules/local/check_barcode.nf

@@ -2,10 +2,10 @@ process CHECK_BARCODE {
     tag "${meta.id}"
     label 'process_low'
 
-    conda "conda-forge::python=3.9 conda-forge::pandas=1.5.2"
+    conda "conda-forge::python=3.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pandas:1.5.2' :
-        'quay.io/biocontainers/pandas:1.5.2' }"
+        'https://depot.galaxyproject.org/singularity/python:3.9' :
+        'biocontainers/python:3.9' }"
 
     input:
     tuple val(meta)     , path(barcodes)
@@ -27,6 +27,7 @@ process CHECK_BARCODE {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
         pacbio_barcode_check: \$(pacbio_barcode_check.py -v)
     END_VERSIONS
     """
@@ -37,6 +38,7 @@ process CHECK_BARCODE {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
         pacbio_barcode_check: \$(pacbio_barcode_check.py -v)
     END_VERSIONS
     """

modules/local/extract_contaminants.nf

@@ -2,10 +2,10 @@ process EXTRACT_CONTAMINANTS {
     tag "${meta.id}"
     label 'process_low'
 
-    conda "conda-forge::python=3.9 conda-forge::pandas=1.5.2"
+    conda "conda-forge::python=3.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pandas:1.5.2' :
-        'quay.io/biocontainers/pandas:1.5.2' }"
+        'https://depot.galaxyproject.org/singularity/python:3.9' :
+        'biocontainers/python:3.9' }"
 
     input:
     tuple val(meta), path(fasta)
@@ -24,6 +24,7 @@ process EXTRACT_CONTAMINANTS {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
         extract_contaminants_by_type: \$(extract_contaminants_by_type.py -v)
     END_VERSIONS
     """
@@ -35,6 +36,7 @@ process EXTRACT_CONTAMINANTS {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
         extract_contaminants_by_type: \$(extract_contaminants_by_type.py -v)
     END_VERSIONS
     """

modules/local/filter_barcode.nf

@@ -2,10 +2,10 @@ process FILTER_BARCODE {
     tag "${meta.id}"
     label 'process_low'
 
-    conda "conda-forge::python=3.9 conda-forge::pandas=1.5.2"
+    conda "conda-forge::python=3.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pandas:1.5.2' :
-        'quay.io/biocontainers/pandas:1.5.2' }"
+        'https://depot.galaxyproject.org/singularity/python:3.9' :
+        'biocontainers/python:3.9' }"
 
     input:
     tuple val(meta), path(fasta)
@@ -28,6 +28,7 @@ process FILTER_BARCODE {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
         filter_barcode_blast_results: \$(filter_barcode_blast_results.py -v)
     END_VERSIONS
     """
@@ -41,6 +42,7 @@ process FILTER_BARCODE {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
         filter_barcode_blast_results: \$(filter_barcode_blast_results.py -v)
     END_VERSIONS
     """

modules/local/format_diamond_outfmt6.nf

@@ -2,10 +2,10 @@ process REFORMAT_FULL_OUTFMT6 {
     tag "${meta.id}"
     label 'process_low'
 
-    conda "conda-forge::python=3.9 conda-forge::pandas=1.5.2"
+    conda "conda-forge::python=3.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pandas:1.5.2' :
-        'quay.io/biocontainers/pandas:1.5.2' }"
+        'https://depot.galaxyproject.org/singularity/python:3.9' :
+        'biocontainers/python:3.9' }"
 
     input:
     tuple val(meta), path(diamond_blast)
@@ -21,6 +21,7 @@ process REFORMAT_FULL_OUTFMT6 {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
         reformat_diamond_outfmt6: \$(reformat_diamond_outfmt6.py -v)
     END_VERSIONS
     """
@@ -32,6 +33,7 @@ process REFORMAT_FULL_OUTFMT6 {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
         reformat_diamond_outfmt6: \$(reformat_diamond_outfmt6.py -v)
     END_VERSIONS
     """

modules/local/gc_content.nf

@@ -0,0 +1,39 @@
+process GC_CONTENT {
+    tag "${meta.id}"
+    label 'process_low'
+
+    conda "conda-forge::python=3.9"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/python:3.9' :
+        'biocontainers/python:3.9' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path( "*-gc.txt" ) , emit: txt
+    path "versions.yml"               , emit: versions
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    gc_content.py ${fasta} > ${prefix}-gc.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
+        gc_content: \$(gc_content.py -v)
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch full_coords.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
+        gc_content: \$(gc_content.py -v)
+    END_VERSIONS
+    """
+}

modules/local/get_largest_scaff.nf

@@ -0,0 +1,40 @@
+process GET_LARGEST_SCAFF {
+
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "conda-forge::coreutils=9.1"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+    'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+    'docker.io/ubuntu:20.04' }"
+
+    input:
+    tuple val( meta ), path( file )
+
+    output:
+    env largest_scaff   , emit: scaff_size
+    path "versions.yml" , emit: versions
+
+    shell:
+    def VERSION     = "9.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    $/
+    largest_scaff=`head -n 1 "${file}" | cut -d$'\t' -f2`
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        coreutils: $VERSION
+    END_VERSIONS
+    /$
+
+    stub:
+    def prefix      = task.ext.prefix ?: "${meta.id}"
+    def VERSION     = "9.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    largest_scaff=1000000
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        coreutils: $VERSION
+    END_VERSIONS
+    """
+}

modules/local/get_lineage_for_kraken.nf

@@ -44,6 +44,7 @@ process GET_LINEAGE_FOR_KRAKEN {
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         python: \$(python --version | sed 's/Python //g')
+        pandas: \$(pip list | grep "pandas" | sed 's/[[:blank:]]//g' | sed 's/pandas//g')
         general_purpose_functions.py: \$(general_purpose_functions.py --version | cut -d' ' -f2)
         get_lineage_for_kraken_results.py: \$(get_lineage_for_kraken_results.py --version | cut -d' ' -f2)
     END_VERSIONS