Enhance Onboarding Experience With Technical Onboarding Documentation and Workshops

technical_documentation_examples/metamist_docker/Dockerfile

@@ -0,0 +1,4 @@
+FROM python:3.10-slim
+
+ARG VERSION=${VERSION:-0.3.1}
+RUN pip install fastqe==${VERSION}

technical_documentation_examples/metamist_docker/Dockerfile_bulk

@@ -0,0 +1,15 @@
+FROM debian:buster-slim
+
+ENV MAMBA_ROOT_PREFIX /root/micromamba
+ENV PATH $MAMBA_ROOT_PREFIX/bin:$PATH
+
+ARG VERSION=${VERSION:-0.3.1}
+
+RUN apt-get update && apt-get install -y git wget bash bzip2 zip curl && \
+    rm -r /var/lib/apt/lists/* && \
+    rm -r /var/cache/apt/* && \
+    wget -qO- https://api.anaconda.org/download/conda-forge/micromamba/0.8.2/linux-64/micromamba-0.8.2-he9b6cbd_0.tar.bz2 | tar -xvj -C /usr/local bin/micromamba && \
+    mkdir ${MAMBA_ROOT_PREFIX} && \
+    micromamba install -y --prefix ${MAMBA_ROOT_PREFIX} -c bioconda -c conda-forge \
+    fastqe=${VERSION} google-cloud-sdk && \
+    rm -r /root/micromamba/pkgs

technical_documentation_examples/metamist_docker/test_fastqe.py

@@ -0,0 +1,53 @@
+"""
+Jobs to run FastQE.
+"""
+
+from os.path import basename
+
+import hailtop.batch as hb
+from hailtop.batch.job import Job
+
+from cpg_utils import Path
+from cpg_utils.hail_batch import command
+from cpg_utils.hail_batch import image_path
+from cpg_workflows.filetypes import (
+    BamPath,
+    FastqPath,
+)
+from cpg_workflows.resources import STANDARD
+
+
+def fastqe(
+    b: hb.Batch,
+    output_html_path: Path,
+    output_zip_path: Path,
+    input_path1: BamPath | FastqPath,
+    input_path2: BamPath | FastqPath,
+    job_attrs: dict | None = None,
+) -> Job:
+    """
+    Adds FastQE jobs. If the input is a set of fqs, runs FastQE on each fq file.
+    """
+    j = b.new_job("FASTQE", (job_attrs or {}) | {"tool": "fastqe"})
+    j.image(image_path("fastqe"))
+    threads = STANDARD.set_resources(j, ncpu=16).get_nthreads()
+
+    cmd = ""
+    input_file1: str | hb.ResourceFile = b.read_input(str(input_path1))
+    input_file2: str | hb.ResourceFile = b.read_input(str(input_path2))
+    fname1 = basename(str(input_path1))
+    fname2 = basename(str(input_path2))
+
+    cmd += f"""\
+    mkdir -p $BATCH_TMPDIR/outdir
+    fastqe {input_file1} {input_file2} \\
+    --outdir $BATCH_TMPDIR/outdir
+    ls $BATCH_TMPDIR/outdir
+    ln $BATCH_TMPDIR/outdir/*_fastqe.html {j.out_html}
+    ln $BATCH_TMPDIR/outdir/*_fastqe.zip {j.out_zip}
+    unzip $BATCH_TMPDIR/outdir/*_fastqe.zip
+    """
+    j.command(command(cmd, monitor_space=True))
+    b.write_output(j.out_html, str(output_html_path))
+    b.write_output(j.out_zip, str(output_zip_path))
+    return j

technical_documentation_examples/metamist_docker/test_fq_r1.fq

@@ -0,0 +1,12 @@
+@Read1_r1
+GTGCCAGCCGCCGCGGTAGTCCGACGTGGC
++
+GGGGGGGGGGGGGGGGGGGGGG!@#$%&%(
+@Read2_r1
+GTGCCAGCCGCCGCGGTAGTCCGACGTGGC
++
+GGGGGGGGGGGGGG!@#$%&%(!@#$%&%(
+@Read3_r1
+GTGCCAGCCGCCGCGGTAGTCCGACGTGGC
++
+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

technical_documentation_examples/metamist_docker/test_fq_r2.fq

@@ -0,0 +1,12 @@
+@Read1_r2
+GTGCCAGCCGCCGCGGTAGTCCGACGTGGC
++
+GGGGGGGGGGGGGGGGGGGGGG!@#$%&%(
+@Read2_r2
+GTGCCAGCCGCCGCGGTAGTCCGACGTGGC
++
+GGGGGGGGGGGGGG!@#$%&%(!@#$%&%(
+@Read3_r2
+GTGCCAGCCGCCGCGGTAGTCCGGGGGGGG
++
+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG