From 34c98a39f675faa1a49d667baa8a9d9eedf6b69f Mon Sep 17 00:00:00 2001 From: Anthony Gagnon Date: Mon, 18 Nov 2024 01:54:47 +0000 Subject: [PATCH] [FIX] formatted samplesheets + fix ci action + configs --- .github/workflows/ci.yml | 2 +- .nf-core.yml | 4 ++-- nextflow.config | 2 +- nextflow_schema.json | 1 - tests/data/samplesheet_testconn.csv | 4 ++-- tests/data/samplesheet_testconn_nometrics.csv | 4 ++-- tests/data/samplesheet_testtracking.csv | 4 ++-- tests/data/samplesheet_testtracking_infant.csv | 4 ++-- tests/data/samplesheet_testtracking_infant_norev.csv | 4 ++-- tests/data/samplesheet_testtracking_infant_not2.csv | 4 ++-- tests/data/samplesheet_testtracking_infant_nowmmask.csv | 4 ++-- tests/data/samplesheet_testtracking_nodwi.csv | 4 ++-- tests/data/samplesheet_testtracking_norev.csv | 4 ++-- 13 files changed, 22 insertions(+), 23 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index fc60216..164604b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -74,4 +74,4 @@ jobs: - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}" run: | - nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results + nf-test test ${GITHUB_WORKSPACE} --profile ${{ matrix.profile }} diff --git a/.nf-core.yml b/.nf-core.yml index c19c236..1c59161 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -9,8 +9,8 @@ lint: - .github/workflows/awstest.yml - .github/workflows/awsfulltest.yml - conf/igenomes.config - - assets/FS_BN_GL_SF_utils/** - - assets/templates/** + - assets/FS_BN_GL_SF_utils/**/* + - assets/templates/**/* files_unchanged: - CODE_OF_CONDUCT.md - assets/nf-core-pediatric_logo_light.png diff --git a/nextflow.config b/nextflow.config index a2c08bd..c2ddaa8 100644 --- a/nextflow.config +++ b/nextflow.config @@ -224,7 +224,7 @@ params { help_full = false show_hidden = false version = false - pipelines_testdata_base_path = "${projectDir}/assets/data/" + pipelines_testdata_base_path = "${projectDir}/tests/data/" // Config options config_profile_name = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 0ede047..318ac1a 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1257,7 +1257,6 @@ "type": "string", "fa_icon": "far fa-check-circle", "description": "Base URL or local path to location of pipeline test dataset files", - "default": "https://raw.githubusercontent.com/nf-core/test-datasets/", "hidden": true } } diff --git a/tests/data/samplesheet_testconn.csv b/tests/data/samplesheet_testconn.csv index 3857e6e..dc5d6ba 100644 --- a/tests/data/samplesheet_testconn.csv +++ b/tests/data/samplesheet_testconn.csv @@ -1,2 +1,2 @@ -subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics -sub-test,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/t1.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/dwi.bvec,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/labels.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/tracking.trk,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/peaks.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/fodf.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/0GenericAffine.mat,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/output1Warp.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/metrics/ \ No newline at end of file +subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics +sub-test,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/t1.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/dwi.bvec,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/labels.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/tracking.trk,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/peaks.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/fodf.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/0GenericAffine.mat,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/output1Warp.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-testconn/metrics/, diff --git a/tests/data/samplesheet_testconn_nometrics.csv b/tests/data/samplesheet_testconn_nometrics.csv index ea7b626..c396c14 100644 --- a/tests/data/samplesheet_testconn_nometrics.csv +++ b/tests/data/samplesheet_testconn_nometrics.csv @@ -1,2 +1,2 @@ -subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics -sub-test,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t1.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/labels.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/tracking.trk,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/peaks.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/fodf.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/0GenericAffine.mat,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/output1Warp.nii.gz, \ No newline at end of file +subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics +sub-test,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t1.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/labels.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/tracking.trk,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/peaks.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/fodf.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/0GenericAffine.mat,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/output1Warp.nii.gz,, diff --git a/tests/data/samplesheet_testtracking.csv b/tests/data/samplesheet_testtracking.csv index 47b10b9..a42d100 100644 --- a/tests/data/samplesheet_testtracking.csv +++ b/tests/data/samplesheet_testtracking.csv @@ -1,2 +1,2 @@ -subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics -sub-test,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t1.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/rev_b0.nii.gz,,,,,,,, \ No newline at end of file +subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics +sub-test,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t1.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/rev_b0.nii.gz,,,,,,,,, diff --git a/tests/data/samplesheet_testtracking_infant.csv b/tests/data/samplesheet_testtracking_infant.csv index 82cdd71..f98c11f 100644 --- a/tests/data/samplesheet_testtracking_infant.csv +++ b/tests/data/samplesheet_testtracking_infant.csv @@ -1,2 +1,2 @@ -subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics -sub-test,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t2.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/rev_b0.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/wm_mask.nii.gz,,,,,, \ No newline at end of file +subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics +sub-test,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t2.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/rev_b0.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/wm_mask.nii.gz,,,,,,, diff --git a/tests/data/samplesheet_testtracking_infant_norev.csv b/tests/data/samplesheet_testtracking_infant_norev.csv index 8407264..8d5f9f2 100644 --- a/tests/data/samplesheet_testtracking_infant_norev.csv +++ b/tests/data/samplesheet_testtracking_infant_norev.csv @@ -1,2 +1,2 @@ -subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics -sub-test,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t2.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/wm_mask.nii.gz,,,,,, \ No newline at end of file +subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics +sub-test,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t2.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/wm_mask.nii.gz,,,,,,, diff --git a/tests/data/samplesheet_testtracking_infant_not2.csv b/tests/data/samplesheet_testtracking_infant_not2.csv index badf66e..e93e33b 100644 --- a/tests/data/samplesheet_testtracking_infant_not2.csv +++ b/tests/data/samplesheet_testtracking_infant_not2.csv @@ -1,2 +1,2 @@ -subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics -sub-test,,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/rev_b0.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/wm_mask.nii.gz,,,,,, \ No newline at end of file +subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics +sub-test,,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/rev_b0.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/wm_mask.nii.gz,,,,,,, diff --git a/tests/data/samplesheet_testtracking_infant_nowmmask.csv b/tests/data/samplesheet_testtracking_infant_nowmmask.csv index f18f84b..4bef056 100644 --- a/tests/data/samplesheet_testtracking_infant_nowmmask.csv +++ b/tests/data/samplesheet_testtracking_infant_nowmmask.csv @@ -1,2 +1,2 @@ -subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics -sub-test,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t2.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/rev_b0.nii.gz,,,,,,,, \ No newline at end of file +subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics +sub-test,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t2.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/rev_b0.nii.gz,,,,,,,,, diff --git a/tests/data/samplesheet_testtracking_nodwi.csv b/tests/data/samplesheet_testtracking_nodwi.csv index 3084e01..4c71821 100644 --- a/tests/data/samplesheet_testtracking_nodwi.csv +++ b/tests/data/samplesheet_testtracking_nodwi.csv @@ -1,2 +1,2 @@ -subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics -sub-test,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t1.nii.gz,,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/rev_b0.nii.gz,,,,,,,, \ No newline at end of file +subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics +sub-test,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t1.nii.gz,,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/rev_b0.nii.gz,,,,,,,,, diff --git a/tests/data/samplesheet_testtracking_norev.csv b/tests/data/samplesheet_testtracking_norev.csv index f66edb8..d1b55bb 100644 --- a/tests/data/samplesheet_testtracking_norev.csv +++ b/tests/data/samplesheet_testtracking_norev.csv @@ -1,2 +1,2 @@ -subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics -sub-test,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t1.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,,,,,,,,, \ No newline at end of file +subject,t1,t2,dwi,bval,bvec,rev_b0,labels,wmparc,trk,peaks,fodf,mat,warp,metrics +sub-test,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/t1.nii.gz,,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.nii.gz,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bval,/Users/anthonygagnon/code/nf-pediatric/tests/data/sub-test/dwi.bvec,,,,,,,,,,