From 9de3a949e9927c6c69c97601f00e4adaefe91d52 Mon Sep 17 00:00:00 2001 From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu> Date: Sun, 13 Sep 2020 17:05:03 -0500 Subject: [PATCH] Add deriva auth to getRef --- workflow/rna-seq.nf | 29 ++++++++++++++++++++++++----- 1 file changed, 24 insertions(+), 5 deletions(-) diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index d020f1f..3382803 100644 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -29,6 +29,11 @@ params.speciesForce = "" deriva = Channel .fromPath(params.deriva) .ifEmpty { exit 1, "deriva credential file not found: ${params.deriva}" } +deriva.into { + deriva_getBag + deriva_getRefInfer + deriva_getRef +} bdbag = Channel .fromPath(params.bdbag) .ifEmpty { exit 1, "deriva cookie file for bdbag not found: ${params.bdbag}" } @@ -127,7 +132,7 @@ process getBag { publishDir "${outDir}/inputBag", mode: 'copy', pattern: "Replicate_*.zip" input: - path credential, stageAs: "credential.json" from deriva + path credential, stageAs: "credential.json" from deriva_getBag path derivaConfig output: @@ -374,6 +379,7 @@ process getRefInfer { tag "${refName}" input: + path credential, stageAs: "credential.json" from deriva_getRefInfer val refName from referenceInfer output: @@ -385,6 +391,12 @@ process getRefInfer { hostname > ${repRID}.${refName}.getRefInfer.log ulimit -a >> ${repRID}.${refName}.getRefInfer.log + # link credential file for authentication + echo -e "LOG: linking deriva credentials" >> ${repRID}.getRefInfer.log + mkdir -p ~/.deriva + ln -sf `readlink -e credential.json` ~/.deriva/credential.json + echo -e "LOG: linked" >> ${repRID}.getRefInfer.log + # set the reference name if [ "${refName}" == "ERCC" ] then @@ -430,8 +442,8 @@ process getRefInfer { filename=\$(echo \$(basename \${refURL}) | grep -oP '.*(?=:)') deriva-hatrac-cli --host ${referenceBase} get \${refURL} unzip \$(basename \${refURL}) - mkdir -p \${references} - mv \${fName}/* \${references}/ + mv \${fName}/* . + mv bed ${refName}/ fi echo -e "LOG: fetched" >> ${repRID}.${refName}.getRefInfer.log @@ -696,6 +708,7 @@ process getRef { tag "${species}" input: + path credential, stageAs: "credential.json" from deriva_getRef val spike from spikeInfer_getRef val species from speciesInfer_getRef @@ -707,6 +720,12 @@ process getRef { hostname > ${repRID}.getRef.log ulimit -a >> ${repRID}.getRef.log + # link credential file for authentication + echo -e "LOG: linking deriva credentials" >> ${repRID}.getRef.log + mkdir -p ~/.deriva + ln -sf `readlink -e credential.json` ~/.deriva/credential.json + echo -e "LOG: linked" >> ${repRID}.getRef.log + # set the reference name if [ "${species}" == "Mus musculus" ] then @@ -762,8 +781,8 @@ process getRef { filename=\$(echo \$(basename \${refURL}) | grep -oP '.*(?=:)') deriva-hatrac-cli --host ${referenceBase} get \${refURL} unzip \$(basename \${refURL}) - mkdir -p \${references} - mv \${fName}/* \${references}/ + mv \${fName}/* . + mv bed ${refName}/ fi echo -e "LOG: fetched" >> ${repRID}.getRef.log """ -- GitLab