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Standardize wdl description #392
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@@ -7,6 +7,20 @@ import "../../../tasks/Preprocessing/Guppy.wdl" as Guppy | |||
import "../../../tasks/Utility/Finalize.wdl" as FF | |||
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workflow ONTMethylation { | |||
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meta { |
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Thank you!
@@ -14,6 +8,31 @@ import "../../../tasks/Utility/Finalize.wdl" as FF | |||
import "../../../tasks/QC/SampleLevelAlignedMetrics.wdl" as COV | |||
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workflow ONTWholeGenome { | |||
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meta { | |||
description: "A workflow that performs single sample variant calling on Oxford Nanopore reads from one or more flow cells. The workflow merges multiple samples into a single BAM prior to variant calling." |
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Typo: not multiple samples
, but multiple flowcells
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@SHuang-Broad should this be all wdl descriptions or just the ones you pointed out?
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All. I don't think we have multi-sample workflows except two or three for joint calling.
@@ -20,6 +13,30 @@ import "../../../tasks/Transcriptomics/MASSeq.wdl" as MAS | |||
import "../../../tasks/Utility/JupyterNotebooks.wdl" as JUPYTER | |||
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workflow PBFlowcell { | |||
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meta { |
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@jonn-smith can you please add your description of the MASseq part?
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For the genome side, here's my proposed description:
The workflow performs the alignment of an SMRT cell's worth of data to a reference.
For genomic sequencing data, the workflow also optionally performs CCS correction if the data is from a CCS library but did not get corrected on-instrument.
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Long term, we should dis-integrate this workflow and update it to match Revio outputs, which is assumed to be the major working machines down the road.
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@SHuang-Broad how's this:
For MAS-seq transcriptome data, this workflow will determine the most likely MAS-seq model, then it will use that model to annotate, segment, and filter the CCS reads. These CCS reads will then be aligned to the reference in trascriptome alignemnt mode. Note: Currently the MAS-seq workflow separates CLR reads, but does not process them.
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String gcs_out_root_dir | ||
meta { | ||
description: "A workflow that performs single sample genome assembly on PacBio HiFi reads from one or more flow cells. The workflow merges multiple samples into a single BAM prior to genome assembly and variant calling." |
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Let's use SMRT cells
in place of flow cells
.
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Also,
The multiple SMRT cells data are merged prior to assembly.
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@SHuang-Broad should this be all wdl descriptions or just the ones you pointed out?
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For this assembly, just this once.
@@ -14,6 +8,31 @@ import "../../../tasks/Utility/Finalize.wdl" as FF | |||
import "../../../tasks/QC/SampleLevelAlignedMetrics.wdl" as COV | |||
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workflow PBCCSWholeGenome { | |||
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meta { | |||
description: "A workflow that performs single sample variant calling on PacBio HiFi reads from one or more flow cells. The workflow merges multiple samples into a single BAM prior to variant calling." |
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Again, not multiple samples but multiple SMRT cells.
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done
@@ -14,6 +8,25 @@ import "../../../tasks/Utility/Finalize.wdl" as FF | |||
import "../../../tasks/QC/SampleLevelAlignedMetrics.wdl" as COV | |||
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workflow PBCLRWholeGenome { | |||
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meta { | |||
description: "A workflow that performs single sample variant calling on PacBio CLR reads from one or more flow cells. The workflow merges multiple samples into a single BAM prior to variant calling." |
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ditto.
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done
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Some minor changes, then good to go.
# Conflicts: # pipelines/TechAgnostic/Utility/DownloadFromSRA.wdl
# Conflicts: # pipelines/PacBio/Assembly/PBAssembleWithHifiasm.wdl
Edited ./pipeline WDLs such that the workflow description follow the following format: