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use nf-core-gallery bucket
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drernie committed Jan 30, 2024
1 parent cfab6a6 commit 4d51bcf
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3 changes: 2 additions & 1 deletion Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ WRITE_BUCKET ?= quilt-example
FRAGMENT ?= &path=.
NF_DIR ?= ../nextflow
NF_BIN ?= ./launch.sh
PATH_NF ?= ./main.path.nf
PID ?= $$$$
PIPELINE ?= sarek
QUERY ?= ?Name=$(USER)&Owner=Kevin+Moore&Date=2023-03-07&Type=CRISPR&Notebook+URL=http%3A%2F%2Fexample.com
Expand Down Expand Up @@ -67,7 +68,7 @@ pkg-fail: compile

path-input: clean compile #-all
echo "$(TEST_URI)"
$(NF_BIN) run ./main.path.nf -profile standard -plugins $(PROJECT) --outdir "./results"
$(NF_BIN) run $(PATH_NF) -profile standard -plugins $(PROJECT) --outdir "./results"

tower-test: $(NF_BIN)
$(NF_BIN) run "https://github.com/quiltdata/nf-quilt" -name local_einstein -with-tower -r main -latest --pub "$(TEST_URI)"
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29 changes: 29 additions & 0 deletions main.gallery.nf
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@@ -0,0 +1,29 @@
#!/usr/bin/env nextflow
/* groovylint-disable CompileStatic */

nextflow.enable.dsl=2

test_file_local = 'README.md'
test_file_s3 = 's3://nf-core-gallery/nf-core/hlatyping/README_NF_QUILT.md'
test_file_quilt = 'quilt+s3://nf-core-gallery#package=nf-core/hlatyping&path=README_NF_QUILT.md'
// file(test_file_local), file(test_file_s3), file(test_file_quilt)
myFileChannel = Channel.fromList([file(test_file_s3), file(test_file_quilt)])

process CHECK_INPUT {
input:
path input

output:
path 'README_NF_QUILT.md', emit: output

script:
"""
ls -l
echo $input
cp -f $input ../../tmp
"""
}

workflow {
CHECK_INPUT(myFileChannel)
}

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