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alejoe91alejoe91
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build: update to KS 4.1.7
1 parent 0c74dff commit 4171c30

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Lines changed: 13 additions & 13 deletions

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‎pipeline/main.nf‎

Lines changed: 13 additions & 13 deletions
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@@ -1,5 +1,5 @@
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#!/usr/bin/env nextflow
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// hash:sha256:4e75b825c7f8645f69706c859591c0ae36679696401329c1e35d2a41cd5bdd97
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// hash:sha256:ee98b4e65b01a67b4d88307345db45f4e6e8fb4cf31a1015040cf7acaa65e5dd
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// capsule - Job Dispatch Ecephys
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process capsule_aind_ephys_job_dispatch_4 {
@@ -56,7 +56,7 @@ process capsule_aind_ephys_job_dispatch_4 {
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// capsule - Preprocess Ecephys
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process capsule_aind_ephys_preprocessing_1 {
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tag 'capsule-0331265'
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container "$REGISTRY_HOST/published/49b76676-d1f6-4202-9473-c763b2b83563:v12"
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container "$REGISTRY_HOST/published/49b76676-d1f6-4202-9473-c763b2b83563:v13"
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cpus 16
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memory '60 GB'
@@ -87,9 +87,9 @@ process capsule_aind_ephys_preprocessing_1 {
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echo "[${task.tag}] cloning git repo..."
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if [[ "\$(printf '%s\n' "2.20.0" "\$(git version | awk '{print \$3}')" | sort -V | head -n1)" = "2.20.0" ]]; then
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git -c credential.helper= clone --filter=tree:0 --branch v12.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-0331265.git" capsule-repo
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git -c credential.helper= clone --filter=tree:0 --branch v13.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-0331265.git" capsule-repo
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else
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git -c credential.helper= clone --branch v12.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-0331265.git" capsule-repo
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git -c credential.helper= clone --branch v13.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-0331265.git" capsule-repo
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fi
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mv capsule-repo/code capsule/code && ln -s \$PWD/capsule/code /code
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rm -rf capsule-repo
@@ -153,7 +153,7 @@ process capsule_nwb_packaging_ecephys_capsule_12 {
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// capsule - Spikesort Kilosort4 Ecephys
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process capsule_spikesort_kilosort_4_ecephys_7 {
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tag 'capsule-4110207'
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container "$REGISTRY_HOST/published/3372ccfd-0388-4e1e-8c4f-46b470fcf871:v12"
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container "$REGISTRY_HOST/published/3372ccfd-0388-4e1e-8c4f-46b470fcf871:v13"
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cpus 16
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memory '60 GB'
@@ -184,9 +184,9 @@ process capsule_spikesort_kilosort_4_ecephys_7 {
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echo "[${task.tag}] cloning git repo..."
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if [[ "\$(printf '%s\n' "2.20.0" "\$(git version | awk '{print \$3}')" | sort -V | head -n1)" = "2.20.0" ]]; then
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git -c credential.helper= clone --filter=tree:0 --branch v12.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-4110207.git" capsule-repo
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git -c credential.helper= clone --filter=tree:0 --branch v13.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-4110207.git" capsule-repo
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else
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git -c credential.helper= clone --branch v12.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-4110207.git" capsule-repo
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git -c credential.helper= clone --branch v13.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-4110207.git" capsule-repo
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fi
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mv capsule-repo/code capsule/code && ln -s \$PWD/capsule/code /code
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rm -rf capsule-repo
@@ -352,7 +352,7 @@ process capsule_aind_ephys_visualization_6 {
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// capsule - Collect Results Ecephys
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process capsule_aind_ephys_results_collector_9 {
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tag 'capsule-0338545'
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container "$REGISTRY_HOST/published/5b7e48bb-8123-4b4c-b7bf-ebaa2de8555e:v14"
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container "$REGISTRY_HOST/published/5b7e48bb-8123-4b4c-b7bf-ebaa2de8555e:v15"
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cpus 4
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memory '30 GB'
@@ -389,9 +389,9 @@ process capsule_aind_ephys_results_collector_9 {
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echo "[${task.tag}] cloning git repo..."
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if [[ "\$(printf '%s\n' "2.20.0" "\$(git version | awk '{print \$3}')" | sort -V | head -n1)" = "2.20.0" ]]; then
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git -c credential.helper= clone --filter=tree:0 --branch v14.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-0338545.git" capsule-repo
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git -c credential.helper= clone --filter=tree:0 --branch v15.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-0338545.git" capsule-repo
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else
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git -c credential.helper= clone --branch v14.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-0338545.git" capsule-repo
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git -c credential.helper= clone --branch v15.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-0338545.git" capsule-repo
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fi
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mv capsule-repo/code capsule/code && ln -s \$PWD/capsule/code /code
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rm -rf capsule-repo
@@ -459,7 +459,7 @@ process capsule_nwb_packaging_units_11 {
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// capsule - Quality Control Ecephys
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process capsule_quality_control_ecephys_13 {
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tag 'capsule-0625308'
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container "$REGISTRY_HOST/published/56a55c84-3013-4683-be83-14d607d2cfe6:v14"
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container "$REGISTRY_HOST/published/56a55c84-3013-4683-be83-14d607d2cfe6:v15"
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cpus 8
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memory '60 GB'
@@ -488,9 +488,9 @@ process capsule_quality_control_ecephys_13 {
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echo "[${task.tag}] cloning git repo..."
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if [[ "\$(printf '%s\n' "2.20.0" "\$(git version | awk '{print \$3}')" | sort -V | head -n1)" = "2.20.0" ]]; then
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git -c credential.helper= clone --filter=tree:0 --branch v14.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-0625308.git" capsule-repo
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git -c credential.helper= clone --filter=tree:0 --branch v15.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-0625308.git" capsule-repo
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else
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git -c credential.helper= clone --branch v14.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-0625308.git" capsule-repo
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git -c credential.helper= clone --branch v15.0 "https://\$GIT_ACCESS_TOKEN@\$GIT_HOST/capsule-0625308.git" capsule-repo
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fi
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mv capsule-repo/code capsule/code && ln -s \$PWD/capsule/code /code
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rm -rf capsule-repo

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