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Update submodules and rename subworkflow #10

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Update submodules and rename subworkflow #10

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63eb520
Update luslab-nf-modules submodule
mjmansfi Mar 3, 2021
f267e55
Properly rename submodule to subworkflow
mjmansfi Mar 3, 2021
30faacd
Update path in main.nf
mjmansfi Mar 3, 2021
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2 changes: 1 addition & 1 deletion main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ include { filtlong } from "./modules/luslab-nf-modules/tools/filtlong/main.nf"

include { minionqc } from "./modules/luslab-nf-modules/tools/minionqc/main.nf"
include { pairwise_genome_alignment as align_to_self ;
pairwise_genome_alignment as align_to_reference } from "./modules/local/submodule/pairwise_genome_alignment/main.nf"
pairwise_genome_alignment as align_to_reference } from "./modules/local/subworkflow/pairwise_genome_alignment/main.nf"
include { porechop } from "./modules/luslab-nf-modules/tools/porechop/main.nf"
include { tantan ;
tantan_to_GFF3 } from "./modules/luslab-nf-modules/tools/tantan/main.nf"
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0 ...bmodule/pairwise_genome_alignment/main.nf → ...orkflow/pairwise_genome_alignment/main.nf
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0 ...le/pairwise_genome_alignment/test/main.nf → ...ow/pairwise_genome_alignment/test/main.nf
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2 changes: 1 addition & 1 deletion modules/luslab-nf-modules
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Submodule luslab-nf-modules updated 45 files
+1 −1 .github/workflows/docker-build-push.yml
+6 −6 .github/workflows/docker-linting.yml
+1 −1 .github/workflows/modules-testing.yml
+1 −1 .github/workflows/workflow-testing.yml
+29 −1 configs/module-defaults.config
+ − test_data/crosslinks/sample1.xl.bed.gz
+ − test_data/crosslinks/sample2.xl.bed.gz
+ − test_data/crosslinks/sample3.xl.bed.gz
+ − test_data/crosslinks/sample4.xl.bed.gz
+ − test_data/crosslinks/sample5.xl.bed.gz
+ − test_data/crosslinks/sample6.xl.bed.gz
+40 −0 test_data/lambda1000a/lambda_top10.fastq
+9 −0 test_data/r/test.csv
+1 −1 tools/flye/VERSION
+2 −1 tools/flye/main.nf
+2 −2 tools/guppy/Dockerfile.cpu
+2 −2 tools/guppy/Dockerfile.gpu
+1 −1 tools/guppy/VERSION
+1 −1 tools/guppy/main.nf
+1 −1 tools/last/VERSION
+46 −4 tools/last/main.nf
+12 −2 tools/last/test/last.config
+12 −8 tools/last/test/main.nf
+0 −28 tools/paraclu/Dockerfile
+1 −1 tools/paraclu/VERSION
+0 −10 tools/paraclu/environment.yml
+23 −54 tools/paraclu/main.nf
+0 −27 tools/paraclu/temp.py
+19 −11 tools/paraclu/test/main.nf
+3 −1 tools/paraclu/test/nextflow.config
+8 −0 tools/r/Dockerfile
+1 −0 tools/r/VERSION
+60 −0 tools/r/functions.nf
+32 −0 tools/r/main.nf
+49 −0 tools/r/test/bin/test_1.R
+16 −0 tools/r/test/main.nf
+4 −0 tools/r/test/nextflow.config
+1 −0 tools/raven/VERSION
+48 −0 tools/raven/main.nf
+70 −0 tools/raven/test/main.nf
+5 −0 tools/raven/test/nextflow.config
+1 −0 tools/shasta/VERSION
+48 −0 tools/shasta/main.nf
+55 −0 tools/shasta/test/main.nf
+6 −0 tools/shasta/test/nextflow.config