chore: Move test data to test-datasets repo

nf-core · Oct 22, 2024 · 9c65113 · 9c65113
1 parent 5c6b24a
commit 9c65113
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Showing 5 changed files with 6 additions and 6 deletions.
diff --git a/modules/local/grohmm/parametertuning/tests/chm13_gtf.nf.test b/modules/local/grohmm/parametertuning/tests/chm13_gtf.nf.test
@@ -19,7 +19,7 @@ nextflow_process {
                     [],
                 ]
                 input[1] = file(
-                            "https://gist.githubusercontent.com/edmundmiller/f9a31e300a90956d8aaff7ad6105e394/raw/99f6eff1ddb8ca9ac1cd766ea2fed9bb83919fb2/broke.gtf",
+                            "https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/broke.gtf",
                             checkIfExists: true
                             )
                 input[2] = 5

diff --git a/modules/local/grohmm/parametertuning/tests/main.nf.test b/modules/local/grohmm/parametertuning/tests/main.nf.test
@@ -19,7 +19,7 @@ nextflow_process {
                     [],
                 ]
                 input[1] = file(
-                            "https://gist.github.com/edmundmiller/c142801995689ed8d15ebcf40b2fb042/raw/eca3b955312209b5845cca084bb506d5250b3d33/hg19.chr7.refGene.gtf",
+                            "https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/hg19.chr7.refGene.gtf",
                             checkIfExists: true
                             )
                 input[2] = 5

diff --git a/modules/local/grohmm/transcriptcalling/tests/main.nf.test b/modules/local/grohmm/transcriptcalling/tests/main.nf.test
@@ -20,7 +20,7 @@ nextflow_process {
                     [],
                 ]
                 input[1] = file(
-                            "https://gist.github.com/edmundmiller/c142801995689ed8d15ebcf40b2fb042/raw/eca3b955312209b5845cca084bb506d5250b3d33/hg19.chr7.refGene.gtf",
+                            "https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/hg19.chr7.refGene.gtf",
                             checkIfExists: true
                             )
                 """
@@ -50,7 +50,7 @@ nextflow_process {
                     file("${projectDir}/tests/config/tuningparams_small.csv", checkIfExists: true),
                 ]
                 input[1] = file(
-                            "https://gist.github.com/edmundmiller/c142801995689ed8d15ebcf40b2fb042/raw/eca3b955312209b5845cca084bb506d5250b3d33/hg19.chr7.refGene.gtf",
+                            "https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/hg19.chr7.refGene.gtf",
                             checkIfExists: true
                             )
                 """

diff --git a/subworkflows/local/grohmm/tests/main.nf.test b/subworkflows/local/grohmm/tests/main.nf.test
@@ -23,7 +23,7 @@ nextflow_workflow {
                     [],
             ])
                 input[1] = Channel.of([file(
-                "https://gist.github.com/edmundmiller/c142801995689ed8d15ebcf40b2fb042/raw/eca3b955312209b5845cca084bb506d5250b3d33/hg19.chr7.refGene.gtf",
+                "https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/hg19.chr7.refGene.gtf",
                     checkIfExists: true
             )]).first()
                 """

diff --git a/workflows/tests/transcript_indentification/grohmm/only_gff/main.nf.test b/workflows/tests/transcript_indentification/grohmm/only_gff/main.nf.test
@@ -14,7 +14,7 @@ nextflow_pipeline {
                 outdir = "$outputDir"
                 skip_grohmm = false
                 gff = 'https://huggingface.co/datasets/edmundmiller/nascent-test-data/resolve/main/chm13v2.0_RefSeq_Liftoff_v5.1.chr21.gff3.gz'
-                // TODO Use CHM13 Fasta
+                fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/chm13v2.0.chr21.fa.gz'
                 gtf = null
                 bed = null
             }