Ultra-long BAM QC (ONT) and long-read BAM QC (Pacbio) MetaWorkflowRuns (

#36)

CHANGELOG.rst

@@ -3,6 +3,11 @@
 Change Log
 ==========
 
+3.5.0
+=====
+* Add commands to create ultra-long BAM QC (ONT) and long-read BAM QC (Pacbio) MetaWorkflowRuns
+
+
 3.4.1
 =====
 * Update dependencies
@@ -12,6 +17,7 @@ Change Log
 =====
 * Add set_property function to wrangler utils for SMaHT
 
+
 3.3.0
 =====
 * Restructure CLI to create MetaWorkflowRuns and execute wrangler functions

magma_smaht/commands/create_meta_workflow_run.py

@@ -9,6 +9,8 @@
     mwfr_cram_to_fastq_paired_end,
     mwfr_bamqc_short_read,
     mwfr_ubam_qc_long_read,
+    mwfr_ultra_long_bamqc,
+    mwfr_long_read_bamqc
 )
 from magma_smaht.utils import get_auth_key
 
@@ -151,6 +153,38 @@ def qc_short_read_bam(file_accession, auth_env):
     mwfr_bamqc_short_read(file_accession, smaht_key)
 
 
+@cli.command()
+@click.help_option("--help", "-h")
+@click.option("-f", "--file-accession", required=True, type=str, help="File accession")
+@click.option(
+    "-e",
+    "--auth-env",
+    required=True,
+    type=str,
+    help="Name of environment in smaht-keys file",
+)
+def qc_ultra_long_bam(file_accession, auth_env):
+    """QC MWFR for aligned, ultra-long BAMs (ONT)"""
+    smaht_key = get_auth_key(auth_env)
+    mwfr_ultra_long_bamqc(file_accession, smaht_key)
+
+
+@cli.command()
+@click.help_option("--help", "-h")
+@click.option("-f", "--file-accession", required=True, type=str, help="File accession")
+@click.option(
+    "-e",
+    "--auth-env",
+    required=True,
+    type=str,
+    help="Name of environment in smaht-keys file",
+)
+def qc_long_read_bam(file_accession, auth_env):
+    """QC MWFR for aligned, long-read BAMs (PacBio)"""
+    smaht_key = get_auth_key(auth_env)
+    mwfr_long_read_bamqc(file_accession, smaht_key)
+
+
 @cli.command()
 @click.help_option("--help", "-h")
 @click.option(

magma_smaht/create_metawfr.py

@@ -37,6 +37,8 @@
 MWF_NAME_FASTQ_LONG_READ = "long_reads_FASTQ_quality_metrics"
 MWF_NAME_CRAM_TO_FASTQ_PAIRED_END = "cram_to_fastq_paired-end"
 MWF_NAME_BAMQC_SHORT_READ = "paired-end_short_reads_BAM_quality_metrics_GRCh38"
+MWF_NAME_ULTRA_LONG_BAMQC = "ultra-long_reads_BAM_quality_metrics_GRCh38"
+MWF_NAME_LONG_READ_BAMQC = "long_reads_BAM_quality_metrics_GRCh38"
 
 # Input argument names
 INPUT_FILES_R1_FASTQ_GZ = "input_files_r1_fastq_gz"
@@ -269,6 +271,32 @@ def mwfr_bamqc_short_read(file_accession, smaht_key):
     create_and_post_mwfr(mwf["uuid"], None, INPUT_FILES_BAM, mwfr_input, smaht_key)
 
 
+def mwfr_ultra_long_bamqc(file_accession, smaht_key):
+    mwf = get_latest_mwf(MWF_NAME_ULTRA_LONG_BAMQC, smaht_key)
+    print(f"Using MetaWorkflow {mwf[ACCESSION]} ({mwf[ALIASES][0]})")
+    bam_meta = get_metadata(file_accession, smaht_key)
+    bam = [{"file": bam_meta[UUID], "dimension": "0"}]
+
+    mwfr_input = [
+        get_mwfr_file_input_arg(INPUT_FILES_BAM, bam),
+    ]
+
+    create_and_post_mwfr(mwf["uuid"], None, INPUT_FILES_BAM, mwfr_input, smaht_key)
+
+
+def mwfr_long_read_bamqc(file_accession, smaht_key):
+    mwf = get_latest_mwf(MWF_NAME_LONG_READ_BAMQC, smaht_key)
+    print(f"Using MetaWorkflow {mwf[ACCESSION]} ({mwf[ALIASES][0]})")
+    bam_meta = get_metadata(file_accession, smaht_key)
+    bam = [{"file": bam_meta[UUID], "dimension": "0"}]
+
+    mwfr_input = [
+        get_mwfr_file_input_arg(INPUT_FILES_BAM, bam),
+    ]
+
+    create_and_post_mwfr(mwf["uuid"], None, INPUT_FILES_BAM, mwfr_input, smaht_key)
+
+
 ################################################
 #   Helper functions
 ################################################

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "magma-suite"
-version = "3.4.1"
+version = "3.5.0"
 description = "Collection of tools to manage meta-workflows automation."
 authors = ["Michele Berselli <[email protected]>", "Doug Rioux", "Soo Lee", "CGAP team"]
 license = "MIT"