From 3ad21a40532ed9ff59e18dd8bf0e3bf8788b7915 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 4 Jan 2021 18:56:36 -0600
Subject: [PATCH] Fix fail if lint
---
workflow/rna-seq.nf | 10 +++++++++-
1 file changed, 9 insertions(+), 1 deletion(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index a9d3aa7..64a5d1b 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -1979,12 +1979,16 @@ process failExecutionRun {
elif [ ${pipelineError} == true ]
then
pipelineError_details=\$(echo "**Submitted metadata does not match infered:** ")
+ #pipelineError_details=\$(echo "**Submitted metadata does not match infered:**\n ")
+ #pipelineError_details=\$(echo "|Metadata|Submitted value|Inferred value|\n ")
+ #pipelineError_details=\$(echo "|:-:|-:|-:|\n")
if ${pipelineError_ends}
then
if [ "${endsMeta}" == "se" ]
then
endMeta="Single End"
elif [ "${endsMeta}" == "pe" ]
+ then
endMeta="Paired End"
else
endMeta="unknown"
@@ -1998,18 +2002,22 @@ process failExecutionRun {
endInfer="unknown"
fi
pipelineError_details=\$(echo \${pipelineError_details}"Paired_End: submitted value = \""\${endMeta}"\" while inferred value = \""\${endsInfer}"\". ")
+ #pipelineError_details=\$(echo \${pipelineError_details}"|*Paired_End*|"\${endMeta}"|"\${endsInfer}"|\n ")
fi
if ${pipelineError_stranded}
then
pipelineError_details=\$(echo \${pipelineError_details}"Strandedness: submitted value = \"${strandedMeta}\" while inferred value = \"${strandedInfer}\". ")
+ #pipelineError_details=\$(echo \${pipelineError_details}"|*Strandedness*|${strandedMeta}|"${strandedInfer}|\n ")
fi
if ${pipelineError_spike}
then
pipelineError_details=\$(echo \${pipelineError_details}"Used_Spike_Ins: submitted value = \"${spikeMeta}\" while inferred value = \"${spikeInfer}\". ")
+ #pipelineError_details=\$(echo \${pipelineError_details}"|*Used_Spike_Ins*|${spikeMeta}|${spikeInfer}|\n ")
fi
if ${pipelineError_species}
then
- pipelineError_details=\$(echo \${pipelineError_details}"[ Species: submitted value = \"${speciesMeta}\" while inferred value = \"${speciesInfer}\". ")
+ pipelineError_details=\$(echo \${pipelineError_details}"Species: submitted value = \"${speciesMeta}\" while inferred value = \"${speciesInfer}\". ")
+ #pipelineError_details=\$(echo \${pipelineError_details}"|*Species*|${speciesMeta}|"${speciesInfer}|\n ")
fi
pipelineError_details=\$(echo "\${pipelineError_details::-1}"
rid=\$(python3 ${script_uploadExecutionRun_failExecutionRun} -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s Error -d "\${pipelineError_details}" -o ${source} -c \${cookie} -u ${executionRunRID})
--
GitLab