Module/minimap2/1.0

modules/minimap2/1.0/config/default.yaml

@@ -0,0 +1,36 @@
+lcr-modules:
+
+    minimap2:
+
+        # TODO: Update the list of available wildcards, if applicable
+        inputs:
+            # Available wildcards: {seq_type} {genome_build} {sample_id}
+            sample_fastq: "__UPDATE__"
+            reference_build: "__UPDATE__"
+
+        scratch_subdirectories: []
+
+        options:
+            minimap2: '-ax map-ont -L --MD -Y -R "@RG\tID:{sample_id}\tLB:{sample_id}\tPL:ONT\tSM:{sample_id}"'
+            samtools: '-bhS'
+
+        conda_envs:
+            minimap2: "{MODSDIR}/envs/minimap2-2.24.yaml"
+            samtools: "{MODSDIR}/envs/samtools-1.9.yaml"
+
+        threads:
+            minimap2: 4
+            samtools: 1
+
+        resources:
+            minimap2: 
+                mem_mb: 30000
+            samtools:
+                mem_mb: 10000
+
+        pairing_config:
+            promethION:
+                run_paired_tumours: False
+                run_unpaired_tumours_with: "no_normal"
+                run_paired_tumours_as_unpaired: True
+

modules/minimap2/1.0/envs/minimap2-2.24.yaml

@@ -0,0 +1,16 @@
+name: minimap2
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - k8=0.2.5
+  - libgcc-ng=12.2.0
+  - libgomp=12.2.0
+  - libstdcxx-ng=12.2.0
+  - libzlib=1.2.13
+  - minimap2=2.24
+  - zlib=1.2.13
+prefix: /home/hshaalan/miniconda3/envs/minimap2

modules/minimap2/1.0/envs/samtools-1.9.yaml

@@ -0,0 +1 @@
+../../../../envs/samtools/samtools-1.9.yaml

modules/minimap2/1.0/minimap2.smk

@@ -0,0 +1,168 @@
+#!/usr/bin/env snakemake
+
+
+##### ATTRIBUTION #####
+
+
+# Original Author:  Haya Shaalan
+# Module Author:    Haya Shaalan
+# Contributors:     N/A
+
+
+##### SETUP #####
+
+# Import package with useful functions for developing analysis modules
+import oncopipe as op
+
+# Check that the oncopipe dependency is up-to-date. Add all the following lines to any module that uses new features in oncopipe
+min_oncopipe_version="1.0.11"
+import pkg_resources
+try:
+    from packaging import version
+except ModuleNotFoundError:
+    sys.exit("The packaging module dependency is missing. Please install it ('pip install packaging') and ensure you are using the most up-to-date oncopipe version")
+
+# To avoid this we need to add the "packaging" module as a dependency for LCR-modules or oncopipe
+
+current_version = pkg_resources.get_distribution("oncopipe").version
+if version.parse(current_version) < version.parse(min_oncopipe_version):
+    print('\x1b[0;31;40m' + f'ERROR: oncopipe version installed: {current_version}' + '\x1b[0m')
+    print('\x1b[0;31;40m' + f"ERROR: This module requires oncopipe version >= {min_oncopipe_version}. Please update oncopipe in your environment" + '\x1b[0m')
+    sys.exit("Instructions for updating to the current version of oncopipe are available at https://lcr-modules.readthedocs.io/en/latest/ (use option 2)")
+
+# End of dependency checking section
+
+# Setup module and store module-specific configuration in `CFG`
+# `CFG` is a shortcut to `config["lcr-modules"]["minimap2"]`
+CFG = op.setup_module(
+    name = "minimap2",
+    version = "1.0",
+    # TODO: If applicable, add more granular output subdirectories
+    subdirectories = ["inputs", "minimap2", "sort_bam", "outputs"],
+)
+
+#include: "../../utils/2.1/utils.smk"
+
+# Define rules to be run locally when using a compute cluster
+localrules:
+    _minimap2_input_fastq,
+    _minimap2_symlink_bam,
+    _minimap2_output_bam,
+    _minimap2_all,
+
+sample_ids_minimap2 = list(CFG['samples']['sample_id'])
+
+##### RULES #####
+
+
+# Symlinks the input files into the module results directory (under '00-inputs/')
+rule _minimap2_input_fastq:
+    input:
+        fastq = CFG["inputs"]["sample_fastq"]
+    output:
+        fastq = CFG["dirs"]["inputs"] + "fastq/{seq_type}/{sample_id}.fastq.gz"
+    run:
+        op.absolute_symlink(input.fastq, output.fastq)
+
+
+rule _minimap2_run:
+    input:
+        fastq = str(rules._minimap2_input_fastq.output.fastq),
+        fasta = reference_files("genomes/{genome_build}/genome_fasta/genome.fa")
+    output:
+        sam = pipe(CFG["dirs"]["minimap2"] + "{seq_type}--{genome_build}/{sample_id}_out.sam")
+    log:
+        stdout = CFG["logs"]["minimap2"] + "{seq_type}--{genome_build}/{sample_id}/minimap2.stdout.log",
+        stderr = CFG["logs"]["minimap2"] + "{seq_type}--{genome_build}/{sample_id}/minimap2.stderr.log"
+    params:
+        opts = CFG["options"]["minimap2"]
+    conda:
+        CFG["conda_envs"]["minimap2"]
+    threads:
+        CFG["threads"]["minimap2"]
+    resources:
+        **CFG["resources"]["minimap2"]
+    shell:
+        op.as_one_line("""
+        minimap2 {params.opts}
+        -t {threads} 
+        {input.fasta} 
+        {input.fastq} 
+        -o {output.sam} 
+        > {log.stdout} 
+        2> {log.stderr}
+        """)
+
+
+rule _minimap2_samtools:
+    input:
+        sam = str(rules._minimap2_run.output.sam)
+    output:
+        bam = CFG["dirs"]["minimap2"] + "{seq_type}--{genome_build}/{sample_id}_out.bam",
+        complete = touch(CFG["dirs"]["minimap2"] + "{seq_type}--{genome_build}/{sample_id}_out.bam.complete")
+    log:
+        stderr = CFG["logs"]["minimap2"] + "{seq_type}--{genome_build}/{sample_id}/samtools.stderr.log"
+    params:
+        opts = CFG["options"]["samtools"]
+    conda:
+        CFG["conda_envs"]["samtools"]
+    threads:
+        CFG["threads"]["samtools"]
+    resources:
+        **CFG["resources"]["samtools"]
+    shell:
+        op.as_one_line("""
+        samtools view {params.opts}
+        {input.sam} > {output.bam} 
+        2> {log.stderr}
+        """)
+
+
+rule _minimap2_symlink_bam:
+    input:
+        bam = str(rules._minimap2_samtools.output.bam)
+    output:
+        bam = CFG["dirs"]["sort_bam"] + "{seq_type}--{genome_build}/{sample_id}.bam"
+    wildcard_constraints: 
+        sample_id = "|".join(sample_ids_minimap2)
+    run:
+        op.absolute_symlink(input.bam, output.bam)
+
+
+# Symlinks the final output files into the module results directory (under '99-outputs/')
+rule _minimap2_output_bam:
+    input:
+        bam = CFG["dirs"]["sort_bam"] + "{seq_type}--{genome_build}/{sample_id}.sort.bam",
+        bai = CFG["dirs"]["sort_bam"] + "{seq_type}--{genome_build}/{sample_id}.sort.bam.bai",
+        sorted_bam = str(rules._minimap2_symlink_bam.input.bam)
+    output:
+        bam = CFG["dirs"]["outputs"] + "bam/{seq_type}--{genome_build}/{sample_id}.bam"
+    wildcard_constraints: 
+        sample_id = "|".join(sample_ids_minimap2)
+    run:
+        op.relative_symlink(input.bam, output.bam, in_module=True)
+        op.relative_symlink(input.bai, output.bam + ".bai", in_module=True)
+        os.remove(input.sorted_bam)
+        shell("touch {input.sorted_bam}.deleted")
+
+
+
+# Generates the target sentinels for each run, which generate the symlinks
+rule _minimap2_all:
+    input:
+        expand(
+            [
+                str(rules._minimap2_output_bam.output.bam),
+            ],
+            zip,  # Run expand() with zip(), not product()
+            seq_type=CFG["samples"]["seq_type"],
+            genome_build=CFG["inputs"]["reference_build"],
+            sample_id=CFG["samples"]["sample_id"])
+
+
+##### CLEANUP #####
+
+
+# Perform some clean-up tasks, including storing the module-specific
+# configuration on disk and deleting the `CFG` variable
+op.cleanup_module(CFG)

modules/minimap2/1.0/schemas/base-1.0.yaml

@@ -0,0 +1 @@
+../../../../schemas/base/base-1.0.yaml

modules/minimap2/CHANGELOG.md

@@ -0,0 +1,14 @@
+# Changelog
+
+All notable changes to the `minimap2` module will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [1.0] - 2023-03-14
+
+This release was authored by Haya Shaalan.
+
+<!-- TODO: Explain each important module design decision below. -->
+
+- No module design decisions explained here yet.

modules/utils/2.1/config/default.yaml

@@ -13,7 +13,7 @@ lcr-modules:
 ## Lines commented out with `#?` can optionally be user-configured
 ## Lines commented out with `##` act as regular comments
 
-        paired_modules: ["bwa_mem", "star"]
+        paired_modules: ["bwa_mem", "star", minimap2]
         ## See main README.md for how to set `samples` in the Snakefile
         #! samples: null