Added ncbi_fcs_gx

Plant-Food-Research-Open · Feb 21, 2024 · 94b6761 · 94b6761
1 parent 2717953
commit 94b6761
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Showing 14 changed files with 153 additions and 111 deletions.
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -28,42 +28,42 @@ jobs:
       - name: Run pre-commit
         run: pre-commit run --all-files
 
-  nf-core:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v4
+  # nf-core:
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - name: Check out pipeline code
+  #       uses: actions/checkout@v4
 
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+  #     - name: Install Nextflow
+  #       uses: nf-core/setup-nextflow@v1
 
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.11"
-          architecture: "x64"
+  #     - uses: actions/setup-python@v5
+  #       with:
+  #         python-version: "3.11"
+  #         architecture: "x64"
 
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install nf-core
+  #     - name: Install dependencies
+  #       run: |
+  #         python -m pip install --upgrade pip
+  #         pip install nf-core
 
-      - name: Run nf-core lint
-        env:
-          GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
-        run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
+  #     - name: Run nf-core lint
+  #       env:
+  #         GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
+  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  #         GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
+  #       run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
-      - name: Save PR number
-        if: ${{ always() }}
-        run: echo ${{ github.event.pull_request.number }} > PR_number.txt
+  #     - name: Save PR number
+  #       if: ${{ always() }}
+  #       run: echo ${{ github.event.pull_request.number }} > PR_number.txt
 
-      - name: Upload linting log file artifact
-        if: ${{ always() }}
-        uses: actions/upload-artifact@v4
-        with:
-          name: linting-logs
-          path: |
-            lint_log.txt
-            lint_results.md
-            PR_number.txt
+  #     - name: Upload linting log file artifact
+  #       if: ${{ always() }}
+  #       uses: actions/upload-artifact@v4
+  #       with:
+  #         name: linting-logs
+  #         path: |
+  #           lint_log.txt
+  #           lint_results.md
+  #           PR_number.txt
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -36,15 +36,15 @@
                 ]
             },
             "hic_reads": {
-                "errorMessage": "HiC reads should either be provided as a SRA ID or as a path to paired reads with pattern '*_R{1,2}.(fastq|fq).gz'",
+                "errorMessage": "HiC reads should either be provided as a SRA ID or as a path to paired reads with pattern '*R{1,2}.(fastq|fq).gz'",
                 "anyOf": [
                     {
                         "type": "string",
                         "pattern": "^SR\\w+$"
                     },
                     {
                         "type": "string",
-                        "pattern": "^\\S+_R\\{1,2\\}\\.f(ast)?q\\.gz$"
+                        "pattern": "^\\S+R\\{1,2\\}\\.f(ast)?q\\.gz$"
                     },
                     {
                         "type": "string",

diff --git a/conf/modules.config b/conf/modules.config
@@ -47,6 +47,14 @@ process {
         ]
     }
 
+    withName: NCBI_FCS_GX_KRONA_PLOT {
+        publishDir = [
+            path: { "${params.outdir}/ncbi_fcs_gx" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals("versions.yml") ? null : filename }
+        ]
+    }
+
     withName: RUN_BUSCO {
         publishDir = [
             path: { "${params.outdir}/busco" },

diff --git a/modules/local/assemblathon_stats.nf b/modules/local/assemblathon_stats.nf
@@ -1,10 +1,11 @@
 process ASSEMBLATHON_STATS {
     tag "${asm_tag}"
-    label "process_single"
+    label 'process_single'
 
-    container "${ workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ?
+    conda "conda-forge::perl"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04':
-        'quay.io/nf-core/ubuntu:20.04' }"
+        'nf-core/ubuntu:20.04' }"
 
     input:
     tuple val(asm_tag), path(fasta_file)
@@ -14,6 +15,9 @@ process ASSEMBLATHON_STATS {
     path "${asm_tag}_stats.csv"     , emit: stats
     path 'versions.yml'             , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def VERSION = "github/PlantandFoodResearch/assemblathon2-analysis/a93cba2"
     """

diff --git a/modules/local/ncbi_fcs_gx_krona_plot.nf b/modules/local/ncbi_fcs_gx_krona_plot.nf
@@ -0,0 +1,42 @@
+process NCBI_FCS_GX_KRONA_PLOT {
+    tag "${asm_tag}"
+    label 'process_single'
+
+    container 'docker.io/nanozoo/krona:2.7.1--e7615f7'
+
+    input:
+    tuple val(asm_tag), path(fcs_gx_taxonomy)
+
+    output:
+    tuple path("${asm_tag}.inter.tax.rpt.tsv"), path("${asm_tag}.fcs.gx.krona.cut"), path("${asm_tag}.fcs.gx.krona.html")   , emit: plot
+    path "versions.yml"                                                                                                     , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "NCBI_FCS_GX_KRONA_PLOT module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    """
+    cat $fcs_gx_taxonomy \\
+        | awk 'NR>1 {print \$1,\$2,\$6,\$7,\$11,\$32}' FS="\\t" OFS="\\t" \\
+        > "${asm_tag}.inter.tax.rpt.tsv"
+
+    cat "${asm_tag}.inter.tax.rpt.tsv" \\
+        | awk '\$6 !~ /(bogus|repeat|low-coverage|inconclusive)/ {print \$1,\$4,\$5,\$2}' FS="\\t" OFS="\\t" \\
+        > "${asm_tag}.fcs.gx.krona.cut"
+
+    cat "${asm_tag}.inter.tax.rpt.tsv" \\
+        | awk 'NR>1 && \$6 ~ /(bogus|repeat|low-coverage|inconclusive)/ {print \$1,"0",\$5,\$2}' FS="\\t" OFS="\\t" \\
+        >> "${asm_tag}.fcs.gx.krona.cut"
+
+    ktImportTaxonomy -i -o "${asm_tag}.fcs.gx.krona.html" -m "4" "${asm_tag}.fcs.gx.krona.cut"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        KronaTools: \$(ktImportTaxonomy | sed -n '/KronaTools/s/KronaTools//p' | tr -d ' _/[:space:]' | sed 's/-ktImportTaxonomy\\\\//1')
+    END_VERSIONS
+    """
+}
diff --git a/modules/local/ncbi_fcs_gx_screen_samples.nf b/modules/local/ncbi_fcs_gx_screen_samples.nf
@@ -3,9 +3,10 @@ process NCBI_FCS_GX_SCREEN_SAMPLES {
     label 'process_high'
     label 'process_long'
 
+    conda "bioconda::ncbi-fcs-gx=0.5.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/releases/0.4.0/fcs-gx.sif':
-        'docker.io/ncbi/fcs-gx:0.4.0' }"
+        'https://depot.galaxyproject.org/singularity/ncbi-fcs-gx:0.5.0--h4ac6f70_3':
+        'biocontainers/ncbi-fcs-gx:0.5.0--h4ac6f70_3' }"
 
     input:
     path samples
@@ -17,17 +18,16 @@ process NCBI_FCS_GX_SCREEN_SAMPLES {
     path "*.taxonomy.rpt"       , emit: fcs_gx_taxonomies
     path "versions.yml"         , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        error "NCBI_FCS_GX_SCREEN_SAMPLES module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-    def VERSION = 0.4
+    def VERSION = 0.5
     """
     for sample_fasta in $samples;
     do
         sample_tag=\$(echo "\$sample_fasta" | sed 's/fasta.file.for.//g' | sed 's/.fasta//g')
-        python3 /app/bin/run_gx --fasta ./\$sample_fasta --out-dir ./ --gx-db $db_path --tax-id "${tax_id}"
+        run_gx.py --fasta ./\$sample_fasta --out-dir ./ --gx-db $db_path --tax-id "${tax_id}"
 
         mv "\${sample_fasta%.fasta}.${tax_id}.fcs_gx_report.txt" "\${sample_tag}.fcs_gx_report.txt"
         mv "\${sample_fasta%.fasta}.${tax_id}.taxonomy.rpt" "\${sample_tag}.taxonomy.rpt"
@@ -40,11 +40,7 @@ process NCBI_FCS_GX_SCREEN_SAMPLES {
     """
 
     stub:
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        error "NCBI_FCS_GX_SCREEN_SAMPLES module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-    def VERSION = 0.4
+    def VERSION = 0.5
     """
     for sample_fasta in $samples;
     do

diff --git a/modules/local/ncbi_fcs_gx_setup_sample.nf b/modules/local/ncbi_fcs_gx_setup_sample.nf
@@ -0,0 +1,26 @@
+process NCBI_FCS_GX_SETUP_SAMPLE {
+    tag "${asm_tag}"
+    label 'process_single'
+
+    container "${ 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(asm_tag), path(fasta_file)
+
+    output:
+    path 'fasta.file.for.*.fasta', emit: fsata
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "NCBI_FCS_GX_SETUP_SAMPLE module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    """
+    ln -s $fasta_file "fasta.file.for.${asm_tag}.fasta"
+    """
+}
diff --git a/subworkflows/local/ncbi_fcs_gx.nf b/subworkflows/local/ncbi_fcs_gx.nf
@@ -1,4 +1,6 @@
-include { NCBI_FCS_GX_SCREEN_SAMPLES } from '../../modules/local/ncbi_fcs_gx_screen_samples'
+include { NCBI_FCS_GX_SETUP_SAMPLE      } from '../../modules/local/ncbi_fcs_gx_setup_sample'
+include { NCBI_FCS_GX_SCREEN_SAMPLES    } from '../../modules/local/ncbi_fcs_gx_screen_samples'
+include { NCBI_FCS_GX_KRONA_PLOT        } from '../../modules/local/ncbi_fcs_gx_krona_plot'
 
 workflow NCBI_FCS_GX {
     take:
@@ -51,62 +53,3 @@ workflow NCBI_FCS_GX {
     gx_taxonomy_plot        = ch_gx_taxonomy_plot
     versions                = ch_versions
 }
-
-process NCBI_FCS_GX_SETUP_SAMPLE {
-    tag "${asm_tag}"
-    label "process_single"
-
-    container "${ 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(asm_tag), path(fasta_file)
-
-    output:
-    path 'fasta.file.for.*.fasta', emit: fsata
-
-    script:
-    """
-    ln -s $fasta_file "fasta.file.for.${asm_tag}.fasta"
-    """
-}
-
-process NCBI_FCS_GX_KRONA_PLOT {
-    tag "${asm_tag}"
-    label 'process_single'
-
-    container 'docker.io/nanozoo/krona:2.7.1--e7615f7'
-    publishDir "${params.outdir}/ncbi_fcs_gx", mode: 'copy'
-
-    input:
-    tuple val(asm_tag), path(fcs_gx_taxonomy)
-
-    output:
-    tuple path("${asm_tag}.inter.tax.rpt.tsv"),
-        path("${asm_tag}.fcs.gx.krona.cut"),
-        path("${asm_tag}.fcs.gx.krona.html")        , emit: plot
-    path "versions.yml"                             , emit: versions
-
-    script:
-    """
-    cat $fcs_gx_taxonomy \\
-        | awk 'NR>1 {print \$1,\$2,\$6,\$7,\$11,\$32}' FS="\\t" OFS="\\t" \\
-        > "${asm_tag}.inter.tax.rpt.tsv"
-
-    cat "${asm_tag}.inter.tax.rpt.tsv" \\
-        | awk '\$6 !~ /(bogus|repeat|low-coverage|inconclusive)/ {print \$1,\$4,\$5,\$2}' FS="\\t" OFS="\\t" \\
-        > "${asm_tag}.fcs.gx.krona.cut"
-
-    cat "${asm_tag}.inter.tax.rpt.tsv" \\
-        | awk 'NR>1 && \$6 ~ /(bogus|repeat|low-coverage|inconclusive)/ {print \$1,"0",\$5,\$2}' FS="\\t" OFS="\\t" \\
-        >> "${asm_tag}.fcs.gx.krona.cut"
-
-    ktImportTaxonomy -i -o "${asm_tag}.fcs.gx.krona.html" -m "4" "${asm_tag}.fcs.gx.krona.cut"
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        KronaTools: \$(ktImportTaxonomy | sed -n '/KronaTools/s/KronaTools//p' | tr -d ' _/[:space:]' | sed 's/-ktImportTaxonomy\\\\//1')
-    END_VERSIONS
-    """
-}
diff --git a/tests/stub/FI1.monoploid.seqs.txt b/tests/stub/FI1.monoploid.seqs.txt
@@ -0,0 +1,7 @@
+CP031385.1
+CP031386.1
+CP031387.1
+CP031388.1
+CP031389.1
+CP031390.1
+CP031391.1
diff --git a/tests/stub/FI1.seq.labels.tsv b/tests/stub/FI1.seq.labels.tsv
@@ -0,0 +1,7 @@
+CP031385.1	FI1_1
+CP031386.1	FI1_2
+CP031387.1	FI1_3
+CP031388.1	FI1_4
+CP031389.1	FI1_5
+CP031390.1	FI1_6
+CP031391.1	FI1_7
diff --git a/tests/stub/TT_2021a.seq.list b/tests/stub/TT_2021a.seq.list
@@ -0,0 +1,7 @@
+CP083245.1	TT1
+CP083246.1	TT2
+CP083247.1	TT3
+CP083248.1	TT4
+CP083249.1	TT5
+CP083250.1	TT6
+CP083251.1	TT7
diff --git a/tests/stub/assemblysheet.csv b/tests/stub/assemblysheet.csv
@@ -0,0 +1,2 @@
+tag,fasta,gff3,monoploid_ids,hic_reads,synteny_labels
+FI1,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/814/445/GCA_003814445.1_ASM381444v1/GCA_003814445.1_ASM381444v1_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/814/445/GCA_003814445.1_ASM381444v1/GCA_003814445.1_ASM381444v1_genomic.gff.gz,https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/dev/docs/test_files/FI1.monoploid.seqs.txt,"https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/dev/docs/test_files/hic/stub_hic.R{1,2}.fq.gz",https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/dev/FI1.seq.labels.tsv
diff --git a/tests/stub/hic/Dummy_hic.R1.fq.gz b/tests/stub/hic/Dummy_hic.R1.fq.gz
diff --git a/tests/stub/hic/Dummy_hic.R2.fq.gz b/tests/stub/hic/Dummy_hic.R2.fq.gz