diff --git a/Makefile b/Makefile index 4e9d660f..f946b341 100644 --- a/Makefile +++ b/Makefile @@ -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=$(USER)&Owner=Kevin+Moore&Date=2023-03-07&Type=CRISPR&Notebook+URL=http%3A%2F%2Fexample.com @@ -67,7 +68,7 @@ pkg-fail: compile path-input: clean compile #-all echo "$(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)" diff --git a/main.gallery.nf b/main.gallery.nf new file mode 100644 index 00000000..e0cb1bdd --- /dev/null +++ b/main.gallery.nf @@ -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) +}