From 6901c7e830d30b1102f015a1ee4f830dacaed8b5 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Wed, 3 Feb 2021 12:23:07 -0600 Subject: [PATCH 01/14] ci: Fix bowtie_build names with "" --- .github/filters.yml | 4 ++-- tests/software/bowtie/build/test.yml | 2 +- tests/software/bowtie2/build/test.yml | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/filters.yml b/.github/filters.yml index 8bdb79be..9f4a4a2c 100644 --- a/.github/filters.yml +++ b/.github/filters.yml @@ -3,7 +3,7 @@ bowtie_align: - software/bowtie/build/** - tests/software/bowtie/align/** -bowtie_build: +"bowtie_build": - software/bowtie/build/** - tests/software/bowtie/build/** @@ -12,7 +12,7 @@ bowtie2_align: - software/bowtie2/build/** - tests/software/bowtie2/align/** -bowtie2_build: +"bowtie2_build": - software/bowtie2/build/** - tests/software/bowtie2/build/** diff --git a/tests/software/bowtie/build/test.yml b/tests/software/bowtie/build/test.yml index 4b8cfd7a..117d36c8 100644 --- a/tests/software/bowtie/build/test.yml +++ b/tests/software/bowtie/build/test.yml @@ -2,7 +2,7 @@ command: nextflow run ./tests/software/bowtie/build -entry test_bowtie_build -c tests/config/nextflow.config tags: - bowtie - - bowtie_build + - "bowtie_build" files: - path: output/bowtie/bowtie/NC_010473.1.ebwt md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c diff --git a/tests/software/bowtie2/build/test.yml b/tests/software/bowtie2/build/test.yml index d172b5d2..7a2f8de5 100644 --- a/tests/software/bowtie2/build/test.yml +++ b/tests/software/bowtie2/build/test.yml @@ -2,7 +2,7 @@ command: nextflow run ./tests/software/bowtie2/build -entry test_bowtie2_build -c tests/config/nextflow.config tags: - bowtie2 - - bowtie2_build + - "bowtie2_build" files: - path: output/bowtie2/bowtie2/NC_010473.1.bt2 md5sum: 4db22d92e72111a5fbf609b3d9a43015 From 4d58a037f6ee918fca6931630ca9bee89775f6a1 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Wed, 3 Feb 2021 12:28:10 -0600 Subject: [PATCH 02/14] test(bowtie_align): Fix md5sum --- tests/software/bowtie/align/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/software/bowtie/align/test.yml b/tests/software/bowtie/align/test.yml index a941b233..add90d7c 100644 --- a/tests/software/bowtie/align/test.yml +++ b/tests/software/bowtie/align/test.yml @@ -42,6 +42,6 @@ - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt md5sum: f3c398bba5158f4039334a932d79c051 - path: output/bowtie/test.out - md5sum: a23e9a2a76e949aeb3693bcfae41a615 + md5sum: a81cb18024616415a6cec3108a36fccd - path: output/bowtie/test.bam should_exist: true \ No newline at end of file From b058da5856dd89c7a18ac15d86e4901a6b084244 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Wed, 3 Feb 2021 12:43:18 -0600 Subject: [PATCH 03/14] ci: Test buil to see if build is special --- .github/filters.yml | 4 ++-- tests/software/bowtie/build/test.yml | 2 +- tests/software/bowtie2/build/test.yml | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/filters.yml b/.github/filters.yml index 9f4a4a2c..16bc5581 100644 --- a/.github/filters.yml +++ b/.github/filters.yml @@ -3,7 +3,7 @@ bowtie_align: - software/bowtie/build/** - tests/software/bowtie/align/** -"bowtie_build": +bowtie_buil: - software/bowtie/build/** - tests/software/bowtie/build/** @@ -12,7 +12,7 @@ bowtie2_align: - software/bowtie2/build/** - tests/software/bowtie2/align/** -"bowtie2_build": +bowtie2_buil: - software/bowtie2/build/** - tests/software/bowtie2/build/** diff --git a/tests/software/bowtie/build/test.yml b/tests/software/bowtie/build/test.yml index 117d36c8..cdba4932 100644 --- a/tests/software/bowtie/build/test.yml +++ b/tests/software/bowtie/build/test.yml @@ -2,7 +2,7 @@ command: nextflow run ./tests/software/bowtie/build -entry test_bowtie_build -c tests/config/nextflow.config tags: - bowtie - - "bowtie_build" + - bowtie_buil files: - path: output/bowtie/bowtie/NC_010473.1.ebwt md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c diff --git a/tests/software/bowtie2/build/test.yml b/tests/software/bowtie2/build/test.yml index 7a2f8de5..5e9f11bd 100644 --- a/tests/software/bowtie2/build/test.yml +++ b/tests/software/bowtie2/build/test.yml @@ -2,7 +2,7 @@ command: nextflow run ./tests/software/bowtie2/build -entry test_bowtie2_build -c tests/config/nextflow.config tags: - bowtie2 - - "bowtie2_build" + - bowtie2_buil files: - path: output/bowtie2/bowtie2/NC_010473.1.bt2 md5sum: 4db22d92e72111a5fbf609b3d9a43015 From 7dbac4bdefaa6cd5f40c73e76c49051631c8c00f Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Wed, 3 Feb 2021 12:55:15 -0600 Subject: [PATCH 04/14] ci: Test adding another work to test name --- .github/filters.yml | 4 ++-- tests/software/bowtie/build/test.yml | 4 ++-- tests/software/bowtie2/build/test.yml | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/filters.yml b/.github/filters.yml index 16bc5581..8bdb79be 100644 --- a/.github/filters.yml +++ b/.github/filters.yml @@ -3,7 +3,7 @@ bowtie_align: - software/bowtie/build/** - tests/software/bowtie/align/** -bowtie_buil: +bowtie_build: - software/bowtie/build/** - tests/software/bowtie/build/** @@ -12,7 +12,7 @@ bowtie2_align: - software/bowtie2/build/** - tests/software/bowtie2/align/** -bowtie2_buil: +bowtie2_build: - software/bowtie2/build/** - tests/software/bowtie2/build/** diff --git a/tests/software/bowtie/build/test.yml b/tests/software/bowtie/build/test.yml index cdba4932..f0b505e7 100644 --- a/tests/software/bowtie/build/test.yml +++ b/tests/software/bowtie/build/test.yml @@ -1,8 +1,8 @@ -- name: bowtie build +- name: bowtie build test command: nextflow run ./tests/software/bowtie/build -entry test_bowtie_build -c tests/config/nextflow.config tags: - bowtie - - bowtie_buil + - bowtie_build files: - path: output/bowtie/bowtie/NC_010473.1.ebwt md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c diff --git a/tests/software/bowtie2/build/test.yml b/tests/software/bowtie2/build/test.yml index 5e9f11bd..f80dc765 100644 --- a/tests/software/bowtie2/build/test.yml +++ b/tests/software/bowtie2/build/test.yml @@ -1,8 +1,8 @@ -- name: bowtie2 build +- name: bowtie2 build test command: nextflow run ./tests/software/bowtie2/build -entry test_bowtie2_build -c tests/config/nextflow.config tags: - bowtie2 - - bowtie2_buil + - bowtie2_build files: - path: output/bowtie2/bowtie2/NC_010473.1.bt2 md5sum: 4db22d92e72111a5fbf609b3d9a43015 From 9b454416d268721d26cf1bfc5ec3a3b5cb08323b Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Wed, 3 Feb 2021 13:04:06 -0600 Subject: [PATCH 05/14] ci: Test bowtie-build instead of _ --- .github/filters.yml | 4 ++-- tests/software/bowtie/build/test.yml | 2 +- tests/software/bowtie2/build/test.yml | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/filters.yml b/.github/filters.yml index 8bdb79be..2ccc1de8 100644 --- a/.github/filters.yml +++ b/.github/filters.yml @@ -3,7 +3,7 @@ bowtie_align: - software/bowtie/build/** - tests/software/bowtie/align/** -bowtie_build: +bowtie-build: - software/bowtie/build/** - tests/software/bowtie/build/** @@ -12,7 +12,7 @@ bowtie2_align: - software/bowtie2/build/** - tests/software/bowtie2/align/** -bowtie2_build: +bowtie2-build: - software/bowtie2/build/** - tests/software/bowtie2/build/** diff --git a/tests/software/bowtie/build/test.yml b/tests/software/bowtie/build/test.yml index f0b505e7..0dbd1ce9 100644 --- a/tests/software/bowtie/build/test.yml +++ b/tests/software/bowtie/build/test.yml @@ -2,7 +2,7 @@ command: nextflow run ./tests/software/bowtie/build -entry test_bowtie_build -c tests/config/nextflow.config tags: - bowtie - - bowtie_build + - bowtie-build files: - path: output/bowtie/bowtie/NC_010473.1.ebwt md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c diff --git a/tests/software/bowtie2/build/test.yml b/tests/software/bowtie2/build/test.yml index f80dc765..1226ae88 100644 --- a/tests/software/bowtie2/build/test.yml +++ b/tests/software/bowtie2/build/test.yml @@ -2,7 +2,7 @@ command: nextflow run ./tests/software/bowtie2/build -entry test_bowtie2_build -c tests/config/nextflow.config tags: - bowtie2 - - bowtie2_build + - bowtie2-build files: - path: output/bowtie2/bowtie2/NC_010473.1.bt2 md5sum: 4db22d92e72111a5fbf609b3d9a43015 From 0c88ff7458f0ed91851b27d83cc10a54dbed9bc4 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Thu, 4 Feb 2021 01:18:33 +0000 Subject: [PATCH 06/14] Upgrade Singularity and change TMPDIR for pytest output --- .github/workflows/pytest-workflow.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml index 6428c50d..984d0164 100644 --- a/.github/workflows/pytest-workflow.yml +++ b/.github/workflows/pytest-workflow.yml @@ -25,7 +25,7 @@ jobs: matrix: nxf_version: ['20.11.0-edge'] tags: ['${{ fromJson(needs.changes.outputs.modules) }}'] - profile: ['docker'] ## 'conda', 'singularity' + profile: ['docker', 'singularity'] ## 'conda' env: NXF_ANSI_LOG: false steps: @@ -65,7 +65,7 @@ jobs: if: matrix.profile == 'singularity' uses: eWaterCycle/setup-singularity@v5 with: - singularity-version: 3.5.3 + singularity-version: 3.7.1 - name: Setup miniconda if: matrix.profile == 'conda' @@ -80,7 +80,7 @@ jobs: # Test the module - name: Run pytest-workflow - run: PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --wt 2 --kwdof + run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --wt 2 --kwdof - name: Upload logs on failure if: failure() From fe3cb87f6df6c59f0aa0784126705d4218d7b728 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Thu, 4 Feb 2021 01:18:52 +0000 Subject: [PATCH 07/14] Direct download Singularity containers --- tests/config/nextflow.config | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config index 38396a86..baa83417 100644 --- a/tests/config/nextflow.config +++ b/tests/config/nextflow.config @@ -2,13 +2,12 @@ params { outdir = "output/" publish_dir_mode = "copy" enable_conda = false - singularity_pull_docker_container = true + singularity_pull_docker_container = false } if ("$PROFILE" == "singularity") { singularity.enabled = true singularity.autoMounts = true - singularity.runOptions = '-B /tmp/' } else if ("$PROFILE" == "conda") { params.enable_conda = true } else { From ffc218e51b1a95746067f30a8bac879a7ff97d72 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Thu, 4 Feb 2021 01:31:25 +0000 Subject: [PATCH 08/14] Run alllll the testsgit add .github/workflows/pytest-workflow.yml --- .github/workflows/pytest-workflow.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml index 984d0164..9ff6b5f7 100644 --- a/.github/workflows/pytest-workflow.yml +++ b/.github/workflows/pytest-workflow.yml @@ -19,7 +19,7 @@ jobs: runs-on: ubuntu-20.04 name: ${{ matrix.tags }} ${{ matrix.profile }} ${{ matrix.nxf_version }} needs: changes - if: needs.changes.outputs.modules != '[]' + if: needs.changes.outputs.modules == '[]' strategy: fail-fast: false matrix: From 431c699727523124f1d41436203ef7de628ba691 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Wed, 3 Feb 2021 20:06:05 -0600 Subject: [PATCH 09/14] Revert "ci: Test bowtie-build instead of _" This reverts commit 9b454416d268721d26cf1bfc5ec3a3b5cb08323b. --- .github/filters.yml | 4 ++-- tests/software/bowtie/build/test.yml | 2 +- tests/software/bowtie2/build/test.yml | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/filters.yml b/.github/filters.yml index 2ccc1de8..8bdb79be 100644 --- a/.github/filters.yml +++ b/.github/filters.yml @@ -3,7 +3,7 @@ bowtie_align: - software/bowtie/build/** - tests/software/bowtie/align/** -bowtie-build: +bowtie_build: - software/bowtie/build/** - tests/software/bowtie/build/** @@ -12,7 +12,7 @@ bowtie2_align: - software/bowtie2/build/** - tests/software/bowtie2/align/** -bowtie2-build: +bowtie2_build: - software/bowtie2/build/** - tests/software/bowtie2/build/** diff --git a/tests/software/bowtie/build/test.yml b/tests/software/bowtie/build/test.yml index 0dbd1ce9..f0b505e7 100644 --- a/tests/software/bowtie/build/test.yml +++ b/tests/software/bowtie/build/test.yml @@ -2,7 +2,7 @@ command: nextflow run ./tests/software/bowtie/build -entry test_bowtie_build -c tests/config/nextflow.config tags: - bowtie - - bowtie-build + - bowtie_build files: - path: output/bowtie/bowtie/NC_010473.1.ebwt md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c diff --git a/tests/software/bowtie2/build/test.yml b/tests/software/bowtie2/build/test.yml index 1226ae88..f80dc765 100644 --- a/tests/software/bowtie2/build/test.yml +++ b/tests/software/bowtie2/build/test.yml @@ -2,7 +2,7 @@ command: nextflow run ./tests/software/bowtie2/build -entry test_bowtie2_build -c tests/config/nextflow.config tags: - bowtie2 - - bowtie2-build + - bowtie2_build files: - path: output/bowtie2/bowtie2/NC_010473.1.bt2 md5sum: 4db22d92e72111a5fbf609b3d9a43015 From 6fe7b48b5b485f10fa93947f5a1def3952b84ccb Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Wed, 3 Feb 2021 20:08:11 -0600 Subject: [PATCH 10/14] Revert "Run alllll the testsgit add .github/workflows/pytest-workflow.yml" This reverts commit ffc218e51b1a95746067f30a8bac879a7ff97d72. --- .github/workflows/pytest-workflow.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml index 9ff6b5f7..984d0164 100644 --- a/.github/workflows/pytest-workflow.yml +++ b/.github/workflows/pytest-workflow.yml @@ -19,7 +19,7 @@ jobs: runs-on: ubuntu-20.04 name: ${{ matrix.tags }} ${{ matrix.profile }} ${{ matrix.nxf_version }} needs: changes - if: needs.changes.outputs.modules == '[]' + if: needs.changes.outputs.modules != '[]' strategy: fail-fast: false matrix: From d48e8654018256020c3a715b093524e9c4a2fe4a Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Wed, 3 Feb 2021 20:11:24 -0600 Subject: [PATCH 11/14] ci: Use bowtie filter This will cause a bit of duplication, but it appears to work. Still the same logic, because any changes to bowtie*/build will run the align modules also. So the bowtie_align tags may not even be necessary, since we can't seem to get the bowtie*_build tags to kick off on their own anyways. Thank you for coming to my TED talk. --- .github/filters.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/filters.yml b/.github/filters.yml index 8bdb79be..a9fb3498 100644 --- a/.github/filters.yml +++ b/.github/filters.yml @@ -3,7 +3,7 @@ bowtie_align: - software/bowtie/build/** - tests/software/bowtie/align/** -bowtie_build: +bowtie: - software/bowtie/build/** - tests/software/bowtie/build/** @@ -12,7 +12,7 @@ bowtie2_align: - software/bowtie2/build/** - tests/software/bowtie2/align/** -bowtie2_build: +bowtie2: - software/bowtie2/build/** - tests/software/bowtie2/build/** From eb45368a351c15b61934ab4657e7deaa09e4ae9c Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 4 Feb 2021 10:07:44 +0000 Subject: [PATCH 12/14] Update tests/software/bowtie2/build/test.yml --- tests/software/bowtie2/build/test.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/software/bowtie2/build/test.yml b/tests/software/bowtie2/build/test.yml index f80dc765..b0d5052f 100644 --- a/tests/software/bowtie2/build/test.yml +++ b/tests/software/bowtie2/build/test.yml @@ -1,4 +1,4 @@ -- name: bowtie2 build test +- name: bowtie2 build command: nextflow run ./tests/software/bowtie2/build -entry test_bowtie2_build -c tests/config/nextflow.config tags: - bowtie2 @@ -15,4 +15,4 @@ - path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2 md5sum: 4ccfee8857c3b1c69857e5ecdef597aa - path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2 - md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72 \ No newline at end of file + md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72 From 68f9a0b711cf71a367d85b336b05594a1cb56fbb Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 4 Feb 2021 10:08:01 +0000 Subject: [PATCH 13/14] Update tests/software/bowtie/build/test.yml --- tests/software/bowtie/build/test.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/software/bowtie/build/test.yml b/tests/software/bowtie/build/test.yml index f0b505e7..b537fa80 100644 --- a/tests/software/bowtie/build/test.yml +++ b/tests/software/bowtie/build/test.yml @@ -1,4 +1,4 @@ -- name: bowtie build test +- name: bowtie build command: nextflow run ./tests/software/bowtie/build -entry test_bowtie_build -c tests/config/nextflow.config tags: - bowtie @@ -15,4 +15,4 @@ - path: output/bowtie/bowtie/NC_010473.rev.1.ebwt md5sum: 44f719c2fe42e1f35d54e798775846d1 - path: output/bowtie/bowtie/NC_010473.rev.2.ebwt - md5sum: f3c398bba5158f4039334a932d79c051 \ No newline at end of file + md5sum: f3c398bba5158f4039334a932d79c051 From 5aa920eb53d5f12a9ae7b5680965f3969fa92d9c Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 4 Feb 2021 10:19:28 +0000 Subject: [PATCH 14/14] Update tests/software/bowtie/align/test.yml --- tests/software/bowtie/align/test.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/software/bowtie/align/test.yml b/tests/software/bowtie/align/test.yml index add90d7c..2f280b3d 100644 --- a/tests/software/bowtie/align/test.yml +++ b/tests/software/bowtie/align/test.yml @@ -44,4 +44,3 @@ - path: output/bowtie/test.out md5sum: a81cb18024616415a6cec3108a36fccd - path: output/bowtie/test.bam - should_exist: true \ No newline at end of file