Added FQ2HIC subworkflow

Plant-Food-Research-Open · Feb 26, 2024 · f0bc5a6 · f0bc5a6
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Showing 36 changed files with 1,420 additions and 13 deletions.
diff --git a/bin/assembly2bedpe.py b/bin/assembly2bedpe.py
@@ -0,0 +1,47 @@
+#!/usr/bin/env python
+
+import sys
+import pandas as pd
+
+
+def read_assembly_file_cols(assembly_file_name):
+    with open(assembly_file_name, "r") as file:
+        lines = file.readlines()
+
+    list_of_items = [line.replace("\n", "").split(" ") for line in lines]
+    list_of_three_tuples = [items for items in list_of_items if len(items) == 3]
+    list_of_three_tuples_wt = [
+        [x[0], int(x[1]), int(x[2])] for x in list_of_three_tuples
+    ]
+
+    df = pd.DataFrame(list_of_three_tuples_wt)
+    df.columns = ["name", "number", "length"]
+
+    return df
+
+
+def make_bedpe_cols(assembly_file_pd):
+    pd = assembly_file_pd
+    pd["cum_length"] = pd["length"].cumsum()
+    pd["end_index"] = pd["cum_length"] - 1
+
+    start_index = pd["end_index"].shift(periods=1, fill_value=-1) + 1
+    pd["start_index"] = start_index
+
+    return pd
+
+
+def print_bed_pe_file(bed_pe_df):
+    df = bed_pe_df
+    print("chr1\tx1\tx2\tchr2\ty1\ty2\tname\tscore\tstrand1\tstrand2\tcolor")
+    for index, row in df.iterrows():
+        print(
+            f"assembly\t{row['start_index']}\t{row['end_index']}\tassembly\t{row['start_index']}\t{row['end_index']}\t{row['name'].replace('>', '')}\t.\t.\t.\t0,0,255"
+        )
+
+
+if __name__ == "__main__":
+    assembly_file_name = sys.argv[1]
+
+    assembly_file_cols = read_assembly_file_cols(assembly_file_name)
+    print_bed_pe_file(make_bedpe_cols(assembly_file_cols))
diff --git a/bin/hic2html.py b/bin/hic2html.py
@@ -0,0 +1,24 @@
+#!/usr/bin/env python
+
+import sys
+from pathlib import Path
+import os
+
+
+if __name__ == "__main__":
+    hic_file_name = os.path.basename(sys.argv[1])
+
+    projectDir = "/".join(__file__.split("/")[0:-1])
+    html_template_path = Path(
+        f"{projectDir}/report_modules/templates/hic/hic_html_template.html"
+    )
+
+    with open(html_template_path) as f:
+        html_file_lines = "".join(f.readlines())
+
+    filled_template = html_file_lines.replace("HIC_FILE_NAME", hic_file_name).replace(
+        "BEDPE_FILE_NAME",
+        f"{hic_file_name.replace('.hic', '')}.assembly.bedpe",
+    )
+
+    print(filled_template)
diff --git a/bin/report_modules/templates/hic/hic_html_template.html b/bin/report_modules/templates/hic/hic_html_template.html
@@ -0,0 +1,92 @@
+<html>
+    <head>
+        <meta charset="UTF-8" />
+        <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+        <title>HiC Contact Map</title>
+        <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+        <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css" />
+        <link
+            rel="stylesheet"
+            type="text/css"
+            href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/juicebox.css"
+        />
+        <script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/juicebox.min.js"></script>
+        <style>
+            .app-container-wrapper {
+                display: flex;
+                align-items: center;
+                justify-content: center;
+            }
+
+            .header-wrapper {
+                display: flex;
+                align-items: center;
+                justify-content: center;
+            }
+
+            .stats-wrapper {
+                display: flex;
+                align-items: center;
+                justify-content: center;
+            }
+
+            button {
+                background-color: inherit;
+                float: left;
+                border: none;
+                outline: none;
+                cursor: pointer;
+                padding: 14px 16px;
+                transition: 0.3s;
+                font-size: 17px;
+                min-width: 90px;
+                margin: 8px;
+            }
+
+            button:hover {
+                background-color: #ddd;
+            }
+
+            button.active {
+                background-color: rgb(168, 168, 168);
+            }
+
+            .scaffold-heading {
+                font-size: 24px;
+                margin: 8px;
+                font-weight: 500;
+            }
+        </style>
+    </head>
+
+    <body>
+        <div class="app-container-wrapper">
+            <div id="app-container"></div>
+        </div>
+    </body>
+    <script>
+        const currentURLSegments = window.location.href.split("/");
+        currentURLSegments.pop();
+        const baseURL = currentURLSegments.join("/");
+
+        const container = document.getElementById("app-container");
+        const config = {
+            syncDatasets: false,
+            browsers: [
+                {
+                    backgroundColor: "255,255,255",
+                    url: `${baseURL}/HIC_FILE_NAME`,
+                    name: "HIC_FILE_NAME",
+                    state: "1,1,1,0,0,1,NONE",
+                    tracks: [
+                        {
+                            name: "Scaffolds",
+                            url: `${baseURL}/bedpe/BEDPE_FILE_NAME`,
+                        },
+                    ],
+                },
+            ],
+        };
+        juicebox.init(container, config).then(function (hicBrowser) {});
+    </script>
+</html>
diff --git a/conf/base.config b/conf/base.config
@@ -61,6 +61,12 @@ process {
     withName:NCBI_FCS_GX_SCREEN_SAMPLES {
         memory = { check_max( 512.GB * task.attempt, 'memory' ) }
     }
+    withName:BWA_MEM {
+        time   = { check_max( 2.day  * task.attempt, 'time'    ) }
+    }
+    withName:SAMBLASTER {
+        time   = { check_max( 20.h  * task.attempt, 'time'    ) }
+    }
     withName:CUSTOM_DUMPSOFTWAREVERSIONS {
         cache = false
     }

diff --git a/modules.json b/modules.json
@@ -5,6 +5,16 @@
         "[email protected]:PlantandFoodResearch/nxf-modules.git": {
             "modules": {
                 "pfr": {
+                    "bwa/index": {
+                        "branch": "main",
+                        "git_sha": "4b9da80b1e4c16067babd97554bea42d7cd9ca85",
+                        "installed_by": ["fastq_bwa_mem_samblaster"]
+                    },
+                    "bwa/mem": {
+                        "branch": "main",
+                        "git_sha": "835879b8f174bb4d2c5534d0381ffbe62cc1b060",
+                        "installed_by": ["fastq_bwa_mem_samblaster"]
+                    },
                     "cat/cat": {
                         "branch": "main",
                         "git_sha": "4b9da80b1e4c16067babd97554bea42d7cd9ca85",
@@ -59,6 +69,11 @@
                         "branch": "main",
                         "git_sha": "835879b8f174bb4d2c5534d0381ffbe62cc1b060",
                         "installed_by": ["fasta_ltrretriever_lai"]
+                    },
+                    "samblaster": {
+                        "branch": "main",
+                        "git_sha": "73358a6712178b9a67c39f92e65e8144b5880eae",
+                        "installed_by": ["fastq_bwa_mem_samblaster"]
                     }
                 }
             },
@@ -69,6 +84,11 @@
                         "git_sha": "154661d7c1769532ff7b5f11259644ec200dd47d",
                         "installed_by": ["subworkflows"]
                     },
+                    "fastq_bwa_mem_samblaster": {
+                        "branch": "main",
+                        "git_sha": "9639ac9a556898d0f0e8592bff24585c33326458",
+                        "installed_by": ["subworkflows"]
+                    },
                     "gff3_validate": {
                         "branch": "main",
                         "git_sha": "f9b96bf8142a01f0649ff90570fb10aa973504b9",

diff --git a/modules/local/agp2assembly.nf b/modules/local/agp2assembly.nf
@@ -0,0 +1,19 @@
+process AGP2ASSEMBLY {
+    tag "$sample_id_on_tag"
+    label 'process_single'
+
+    container "docker.io/gallvp/juicebox_scripts:a7ae991_ps"
+    publishDir "${params.outdir}/hic/assembly", mode:'copy'
+
+    input:
+    tuple val(sample_id_on_tag), path(agp_file)
+
+    output:
+    tuple val(sample_id_on_tag), path("*.agp.assembly"), emit: assembly
+
+    script:
+    """
+    assembly_tag=\$(echo $sample_id_on_tag | sed 's/.*\\.on\\.//g')
+    agp2assembly.py $agp_file "\${assembly_tag}.agp.assembly"
+    """
+}
diff --git a/modules/local/assembly2bedpe.nf b/modules/local/assembly2bedpe.nf
@@ -0,0 +1,25 @@
+process ASSEMBLY2BEDPE {
+    tag "$sample_id_on_tag"
+    label 'process_single'
+
+    container "docker.io/gallvp/python3npkgs:v0.4"
+    publishDir "${params.outdir}/hic/bedpe", mode:'copy'
+
+    input:
+    tuple val(sample_id_on_tag), path(agp_assembly_file)
+
+    output:
+    tuple val(sample_id_on_tag), path("*.assembly.bedpe"), emit: bedpe
+
+    script:
+    """
+    assembly_tag=\$(echo $sample_id_on_tag | sed 's/.*\\.on\\.//g')
+    assembly2bedpe.py $agp_assembly_file > "\${assembly_tag}.assembly.bedpe"
+    """
+
+    stub:
+    """
+    assembly_tag=\$(echo $sample_id_on_tag | sed 's/.*\\.on\\.//g')
+    touch "\${assembly_tag}.assembly.bedpe"
+    """
+}
diff --git a/modules/local/hic2html.nf b/modules/local/hic2html.nf
@@ -0,0 +1,19 @@
+process HIC2HTML {
+    tag "$sample_id_on_tag"
+    label 'process_single'
+
+    container "docker.io/gallvp/python3npkgs:v0.4"
+    publishDir "${params.outdir}/hic", mode: 'copy'
+
+    input:
+    tuple val(sample_id_on_tag), path(hic_file)
+
+    output:
+    path "*.html", emit: html
+
+    script:
+    """
+    file_name="$hic_file"
+    hic2html.py "$hic_file" > "\${file_name%.*}.html"
+    """
+}
diff --git a/modules/local/hicqc.nf b/modules/local/hicqc.nf
@@ -0,0 +1,37 @@
+process HICQC {
+    tag "$meta.id"
+    label 'process_single'
+
+    publishDir "${params.outdir}/hic/hic_qc", mode:'copy'
+    container "docker.io/gallvp/hic_qc:6881c33_ps"
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("*.pdf")  , emit: pdf
+    path "versions.yml"             , emit: versions
+
+    script:
+    """
+    hic_qc.py \\
+        -n 10000000 \\
+        -b $bam \\
+        --outfile_prefix "$meta.id"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hic_qc.py: \$(hic_qc.py --version)
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch "${meta.id}.pdf"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hic_qc.py: \$(hic_qc.py --version)
+    END_VERSIONS
+    """
+}
diff --git a/modules/local/juicer_sort.nf b/modules/local/juicer_sort.nf
@@ -0,0 +1,22 @@
+process JUICER_SORT {
+    tag "$sample_id_on_tag"
+    label 'process_high'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04':
+        'nf-core/ubuntu:20.04' }"
+
+    input:
+    tuple val(sample_id_on_tag), path(out_links_txt)
+
+    output:
+    tuple val(sample_id_on_tag), path("*sorted.links.txt"), emit: links
+
+    script:
+    """
+    sort --parallel=${task.cpus} \\
+        -k2,2 -k6,6 \\
+        $out_links_txt \\
+        > out.sorted.links.txt
+    """
+}
diff --git a/modules/local/makeagpfromfasta.nf b/modules/local/makeagpfromfasta.nf
@@ -0,0 +1,18 @@
+process MAKEAGPFROMFASTA {
+    tag "$sample_id_on_tag"
+    label 'process_single'
+
+    container "docker.io/gallvp/juicebox_scripts:a7ae991_ps"
+
+    input:
+    tuple val(sample_id_on_tag), path(assembly_fasta)
+
+    output:
+    tuple val(sample_id_on_tag), path("*.agp"), emit: agp
+
+    script:
+    """
+    file_name="$assembly_fasta"
+    makeAgpFromFasta.py $assembly_fasta "\${file_name%%.*}.agp"
+    """
+}
diff --git a/modules/local/matlock_bam2_juicer.nf b/modules/local/matlock_bam2_juicer.nf
@@ -0,0 +1,19 @@
+process MATLOCK_BAM2_JUICER {
+    tag "$sample_id_on_tag"
+    label 'process_single'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/matlock:20181227--h4b03ef3_3':
+        'biocontainers/matlock:20181227--h4b03ef3_3' }"
+
+    input:
+        tuple val(sample_id_on_tag), path(hic_bam_scaffolds)
+
+    output:
+        tuple val(sample_id_on_tag), path("out.links.txt")
+
+    script:
+        """
+        matlock bam2 juicer $hic_bam_scaffolds out.links.txt
+        """
+}