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reproduce fetchngs error
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drernie committed Dec 6, 2024
1 parent 061c8d9 commit d318efb
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8 changes: 8 additions & 0 deletions Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,13 @@ PROJECT ?= nf-quilt
WRITE_BUCKET ?= udp-spec
FRAGMENT ?= &path=.
NF_DIR ?= ../nextflow
NF_GIT ?= $(NF_DIR)/nextflow
NF_BIN ?= ./launch.sh
PID ?= $$$$
PIPELINE ?= sarek
QUERY ?= ?Name=$(USER)&Owner=Kevin+Moore&Date=2023-03-07&Type=CRISPR&Notebook+URL=http%3A%2F%2Fexample.com
VERSION ?= $(shell grep 'Plugin-Version' plugins/$(PROJECT)/src/resources/META-INF/MANIFEST.MF | awk '{ print $$2 }')
NXF_VER ?= $(shell cat VERSION)
TEST_URI ?= quilt+s3://$(WRITE_BUCKET)$(QUERY)\#package=nf-quilt/dest-$(VERSION)$(FRAGMENT)
PIPE_OUT ?= quilt+s3://$(WRITE_BUCKET)\#package=$(PROJECT)/$(PIPELINE)
S3_BASE = s3://$(WRITE_BUCKET)/$(PROJECT)
Expand Down Expand Up @@ -107,6 +109,12 @@ $(PIPELINE): $(NF_BIN) install
$(NF_BIN) pull nf-core/$(PIPELINE)
$(NF_BIN) run nf-core/$(PIPELINE) -profile test,docker -plugins $(PROJECT)@$(VERSION) --outdir "$(PIPE_OUT)"

fetchngs: $(NF_GIT)
NXF_VER=$(NXF_VER) $(NF_GIT) run nf-core/fetchngs -profile test,docker --input wf/ids.csv --outdir "s3://$(WRITE_BUCKET)/nf-quilt/fetchngs"

nf-git-ver: $(NF_GIT)
NXF_VER=$(NXF_VER) $(NF_GIT) -v

#
# Show dependencies
#
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2 changes: 1 addition & 1 deletion VERSION
Original file line number Diff line number Diff line change
@@ -1 +1 @@
23.04.3
24.10.2

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