Add short-read fastqc MetaworkflowRun (#38)

* Add short-read fastqc

* Bump version

Author: alexander-veit

CHANGELOG.rst

@@ -3,6 +3,12 @@
 Change Log
 ==========
 
+3.6.2
+=====
+* Add short_reads_FASTQ_quality_metrics MetaWorkflowRun
+* Rename short read FASTQ MetaWorkflowRun specific for Illumina
+
+
 3.6.1
 =====
 * Use only input files with status `uploaded` when creating MetaWorkflowRuns. (Ignore `retracted` files)

magma_smaht/commands/create_meta_workflow_run.py

@@ -10,7 +10,8 @@
     mwfr_bamqc_short_read,
     mwfr_ubam_qc_long_read,
     mwfr_ultra_long_bamqc,
-    mwfr_long_read_bamqc
+    mwfr_long_read_bamqc,
+    mwfr_short_read_fastqc
 )
 from magma_smaht.utils import get_auth_key
 
@@ -113,12 +114,30 @@ def align_ont(fileset_accession, auth_env):
     type=str,
     help="Name of environment in smaht-keys file",
 )
-def qc_short_read_fastq(fileset_accession, auth_env):
-    """QC MWFR for short-read FASTQs"""
+def qc_short_read_fastq_illumina(fileset_accession, auth_env):
+    """QC MWFR for paired short-read Illumina FASTQs"""
     smaht_key = get_auth_key(auth_env)
     mwfr_fastqc(fileset_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_short_read_fastq(file_accession, auth_env):
+    """QC MWFR for short-read FASTQs"""
+    smaht_key = get_auth_key(auth_env)
+    mwfr_short_read_fastqc(file_accession, smaht_key)
+
+
 @cli.command()
 @click.help_option("--help", "-h")
 @click.option(

magma_smaht/create_metawfr.py

@@ -35,6 +35,7 @@
 MWF_NAME_HIC = "Hi-C_alignment_GRCh38"
 MWF_NAME_FASTQC = "Illumina_FASTQ_quality_metrics"
 MWF_NAME_FASTQ_LONG_READ = "long_reads_FASTQ_quality_metrics"
+MWF_NAME_FASTQ_SHORT_READ = "short_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"
@@ -277,8 +278,8 @@ def mwfr_ubam_qc_long_read(fileset_accession, smaht_key):
     for dim, bam in enumerate(bams):
         files_input.append({"file": bam[UUID], "dimension": f"{dim}"})
 
-    mwfr_input = [get_mwfr_file_input_arg(INPUT_FILES, files_input)]
-    create_and_post_mwfr(mwf[UUID], file_set, INPUT_FILES, mwfr_input, smaht_key)
+    mwfr_input = [get_mwfr_file_input_arg(INPUT_FILES_BAM, files_input)]
+    create_and_post_mwfr(mwf[UUID], file_set, INPUT_FILES_BAM, mwfr_input, smaht_key)
 
 
 def mwfr_bamqc_short_read(file_accession, smaht_key):
@@ -320,6 +321,19 @@ def mwfr_long_read_bamqc(file_accession, smaht_key):
     create_and_post_mwfr(mwf["uuid"], None, INPUT_FILES_BAM, mwfr_input, smaht_key)
 
 
+def mwfr_short_read_fastqc(file_accession, smaht_key):
+    mwf = get_latest_mwf(MWF_NAME_FASTQ_SHORT_READ, smaht_key)
+    print(f"Using MetaWorkflow {mwf[ACCESSION]} ({mwf[ALIASES][0]})")
+    fastq_meta = get_metadata(file_accession, smaht_key)
+    fastq = [{"file": fastq_meta[UUID], "dimension": "0"}]
+
+    mwfr_input = [
+        get_mwfr_file_input_arg(INPUT_FILES_FASTQ_GZ, fastq),
+    ]
+
+    create_and_post_mwfr(mwf["uuid"], None, INPUT_FILES_FASTQ_GZ, mwfr_input, smaht_key)
+
+
 ################################################
 #   Helper functions
 ################################################

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "magma-suite"
-version = "3.6.1"
+version = "3.6.2"
 description = "Collection of tools to manage meta-workflows automation."
 authors = ["Michele Berselli <[email protected]>", "Doug Rioux", "Soo Lee", "CGAP team"]
 license = "MIT"