Standardize wdl description #392

bshifaw · 2023-04-05T15:46:57Z

Edited ./pipeline WDLs such that the workflow description follow the following format:

WorkflowName {

    meta {
        description: "Workflow description"
    }
    parameter_meta {
        input: "Input description"
    }

    input{
    ...
    }
...
}

…ocks

SHuang-Broad · 2023-04-05T20:09:48Z

pipelines/ONT/Epigenomics/ONTMethylation.wdl

@@ -7,6 +7,20 @@ import "../../../tasks/Preprocessing/Guppy.wdl" as Guppy
 import "../../../tasks/Utility/Finalize.wdl" as FF

 workflow ONTMethylation {
+
+    meta {


SHuang-Broad · 2023-04-05T20:11:13Z

pipelines/ONT/VariantCalling/ONTWholeGenome.wdl

@@ -14,6 +8,31 @@ import "../../../tasks/Utility/Finalize.wdl" as FF
 import "../../../tasks/QC/SampleLevelAlignedMetrics.wdl" as COV

 workflow ONTWholeGenome {
+
+    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."


Typo: not multiple samples, but multiple flowcells

@SHuang-Broad should this be all wdl descriptions or just the ones you pointed out?

All. I don't think we have multi-sample workflows except two or three for joint calling.

SHuang-Broad · 2023-04-05T20:12:41Z

pipelines/PacBio/Alignment/PBFlowcell.wdl

@@ -20,6 +13,30 @@ import "../../../tasks/Transcriptomics/MASSeq.wdl" as MAS
 import "../../../tasks/Utility/JupyterNotebooks.wdl" as JUPYTER

 workflow PBFlowcell {
+
+    meta {


@jonn-smith can you please add your description of the MASseq part?

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.

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.

@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.

SHuang-Broad · 2023-04-05T20:19:44Z

pipelines/PacBio/Assembly/PBAssembleWithHifiasm.wdl


-        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."


Let's use SMRT cells in place of flow cells.

Also,

The multiple SMRT cells data are merged prior to assembly.

@SHuang-Broad should this be all wdl descriptions or just the ones you pointed out?

For this assembly, just this once.

SHuang-Broad · 2023-04-05T20:22:15Z

pipelines/PacBio/VariantCalling/PBCCSWholeGenome.wdl

@@ -14,6 +8,31 @@ import "../../../tasks/Utility/Finalize.wdl" as FF
 import "../../../tasks/QC/SampleLevelAlignedMetrics.wdl" as COV

 workflow PBCCSWholeGenome {
+
+    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."


Again, not multiple samples but multiple SMRT cells.

SHuang-Broad · 2023-04-05T20:22:28Z

pipelines/PacBio/VariantCalling/PBCLRWholeGenome.wdl

@@ -14,6 +8,25 @@ import "../../../tasks/Utility/Finalize.wdl" as FF
 import "../../../tasks/QC/SampleLevelAlignedMetrics.wdl" as COV

 workflow PBCLRWholeGenome {
+
+    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."


pipelines/TechAgnostic/Utility/LRConvertBCF.wdl

SHuang-Broad

Some minor changes, then good to go.

# Conflicts: # pipelines/TechAgnostic/Utility/DownloadFromSRA.wdl

# Conflicts: # pipelines/PacBio/Assembly/PBAssembleWithHifiasm.wdl

bshifaw added 3 commits April 5, 2023 10:52

standardized pipeline/ONT workflow meta and parameter_meta bocks

f1a7620

standardized pipeline/pacbio workflow meta and parameter_meta bocks

0e4c2e7

standardized pipeline/techAgnostic workflow meta and parameter_meta b…

09bb301

…ocks

bshifaw added the documentation label Apr 5, 2023

bshifaw requested a review from SHuang-Broad April 5, 2023 15:46

bshifaw self-assigned this Apr 5, 2023

bshifaw marked this pull request as ready for review April 5, 2023 15:50

SHuang-Broad reviewed Apr 5, 2023

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pipelines/TechAgnostic/Utility/LRConvertBCF.wdl Show resolved Hide resolved

SHuang-Broad requested changes Apr 5, 2023

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bshifaw added 2 commits April 7, 2023 10:35

Merge branch 'main' into bs_standardize_wdl_description

0081ec7

# Conflicts: # pipelines/TechAgnostic/Utility/DownloadFromSRA.wdl

minor formatting

74698cf

bshifaw mentioned this pull request Apr 7, 2023

Replace LRConvertBCF workflow with a more efficient and up-to-date solution #395

Open

minor workflow description fixes

87ad08a

bshifaw requested a review from SHuang-Broad April 7, 2023 19:46

bshifaw added 2 commits April 11, 2023 13:16

Updated PBFlowcell.wdl description

eb9273f

Merge branch 'main' into bs_standardize_wdl_description

e1dfd97

# Conflicts: # pipelines/PacBio/Assembly/PBAssembleWithHifiasm.wdl

bshifaw merged commit c134325 into main Apr 11, 2023

bshifaw deleted the bs_standardize_wdl_description branch April 11, 2023 17:57

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Standardize wdl description #392

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Standardize wdl description #392

Standardize wdl description #392

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bshifaw commented Apr 5, 2023

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