From 628bb3f75164bac6e4e8a6dd4ca2d62a20e76307 Mon Sep 17 00:00:00 2001 From: buehlere Date: Mon, 15 May 2023 15:56:04 -0400 Subject: [PATCH 01/13] reqs and cwltool updates reqs set to match aalap's versions cwlttools updated --- cwl-commandlinetools | 2 +- requirements.txt | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/cwl-commandlinetools b/cwl-commandlinetools index 7e71b5a..b1f1494 160000 --- a/cwl-commandlinetools +++ b/cwl-commandlinetools @@ -1 +1 @@ -Subproject commit 7e71b5a5540d2c4068df82a6021ed77f62800220 +Subproject commit b1f149422fd0fdaa72be799e65643709920c2f44 diff --git a/requirements.txt b/requirements.txt index b8a2a1c..e07742b 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,6 +1,7 @@ coloredlogs==15.0.1 pytest==7.2.0 setuptools==65.4.1 -cwltool==3.1.20220628170238 +cwltool==3.1.20230425144158 +toil[cwl]==5.10.0a1 pytest-runner==6.0.0 tox==3.27.1 From 03cf49cd2399dfc4343fabe071db045f60f1c7f7 Mon Sep 17 00:00:00 2001 From: buehlere Date: Mon, 15 May 2023 16:06:04 -0400 Subject: [PATCH 02/13] Update requirements.txt --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index e07742b..8803225 100644 --- a/requirements.txt +++ b/requirements.txt @@ -2,6 +2,6 @@ coloredlogs==15.0.1 pytest==7.2.0 setuptools==65.4.1 cwltool==3.1.20230425144158 -toil[cwl]==5.10.0a1 +toil[cwl] @ git+https://github.com/DataBiosphere/toil.git pytest-runner==6.0.0 tox==3.27.1 From 9421eb65ff7e138f83852292313b27d192246fe1 Mon Sep 17 00:00:00 2001 From: buehlere Date: Tue, 16 May 2023 09:30:19 -0400 Subject: [PATCH 03/13] Update test_nucleo_qc.yaml --- .github/workflows/test_nucleo_qc.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/test_nucleo_qc.yaml b/.github/workflows/test_nucleo_qc.yaml index 9d3f56d..824654a 100644 --- a/.github/workflows/test_nucleo_qc.yaml +++ b/.github/workflows/test_nucleo_qc.yaml @@ -44,6 +44,8 @@ jobs: - name: Install Test data run: | bash install_data.sh + cd cwl-commandlinetools + git checkout hotfix/athena_inputs - name: Pytest run: | tox -vv From be15ab0c69765328f3dce4879badeece0a78fa41 Mon Sep 17 00:00:00 2001 From: buehlere Date: Tue, 16 May 2023 09:36:48 -0400 Subject: [PATCH 04/13] Update test_nucleo_qc.yaml --- .github/workflows/test_nucleo_qc.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/test_nucleo_qc.yaml b/.github/workflows/test_nucleo_qc.yaml index 824654a..b601e6b 100644 --- a/.github/workflows/test_nucleo_qc.yaml +++ b/.github/workflows/test_nucleo_qc.yaml @@ -44,6 +44,8 @@ jobs: - name: Install Test data run: | bash install_data.sh + - name: Checkout specific submodule + run: | cd cwl-commandlinetools git checkout hotfix/athena_inputs - name: Pytest From 2003d71e7bbb9b77c47d2de1d9f8b645af5c4dc6 Mon Sep 17 00:00:00 2001 From: buehlere Date: Tue, 16 May 2023 09:44:08 -0400 Subject: [PATCH 05/13] Update test_nucleo_qc.yaml --- .github/workflows/test_nucleo_qc.yaml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/.github/workflows/test_nucleo_qc.yaml b/.github/workflows/test_nucleo_qc.yaml index b601e6b..3c4d6b9 100644 --- a/.github/workflows/test_nucleo_qc.yaml +++ b/.github/workflows/test_nucleo_qc.yaml @@ -24,7 +24,6 @@ jobs: - name: Checkout uses: actions/checkout@v3 with: - ref: ${{ github.head_ref }} submodules: recursive - name: Set up Python uses: actions/setup-python@v3 @@ -44,10 +43,6 @@ jobs: - name: Install Test data run: | bash install_data.sh - - name: Checkout specific submodule - run: | - cd cwl-commandlinetools - git checkout hotfix/athena_inputs - name: Pytest run: | tox -vv From 237b2a63d944fb19c3a1e0af10202aee30a52ad9 Mon Sep 17 00:00:00 2001 From: buehlere Date: Tue, 16 May 2023 09:52:53 -0400 Subject: [PATCH 06/13] trying to use right submodule --- .github/workflows/test_nucleo_qc.yaml | 1 + .gitmodules | 1 + 2 files changed, 2 insertions(+) diff --git a/.github/workflows/test_nucleo_qc.yaml b/.github/workflows/test_nucleo_qc.yaml index 3c4d6b9..9d3f56d 100644 --- a/.github/workflows/test_nucleo_qc.yaml +++ b/.github/workflows/test_nucleo_qc.yaml @@ -24,6 +24,7 @@ jobs: - name: Checkout uses: actions/checkout@v3 with: + ref: ${{ github.head_ref }} submodules: recursive - name: Set up Python uses: actions/setup-python@v3 diff --git a/.gitmodules b/.gitmodules index 39d1af9..aff6853 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,6 +1,7 @@ [submodule "cwl-commandlinetools"] path = cwl-commandlinetools url = https://github.com/msk-access/cwl-commandlinetools.git + branch = hotfix/athena_inputs [submodule "cwl_subworkflows"] path = cwl_subworkflows url = https://github.com/msk-access/cwl_subworkflows.git From 48124c6140496af80d6138f343fb3aba6460d17b Mon Sep 17 00:00:00 2001 From: buehlere Date: Tue, 16 May 2023 11:14:17 -0400 Subject: [PATCH 07/13] update subworkflows --- .gitmodules | 1 - cwl_subworkflows | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/.gitmodules b/.gitmodules index aff6853..39d1af9 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,7 +1,6 @@ [submodule "cwl-commandlinetools"] path = cwl-commandlinetools url = https://github.com/msk-access/cwl-commandlinetools.git - branch = hotfix/athena_inputs [submodule "cwl_subworkflows"] path = cwl_subworkflows url = https://github.com/msk-access/cwl_subworkflows.git diff --git a/cwl_subworkflows b/cwl_subworkflows index 11668a9..39da215 160000 --- a/cwl_subworkflows +++ b/cwl_subworkflows @@ -1 +1 @@ -Subproject commit 11668a94c15c7eb801e34fef591762505e71ba4c +Subproject commit 39da2152220fa5b41f891b9187d08266906c729b From b5bb0d93df0cb88a7a75e2ac4089988eafb8f00a Mon Sep 17 00:00:00 2001 From: buehlere Date: Tue, 16 May 2023 11:21:45 -0400 Subject: [PATCH 08/13] update --- .gitmodules | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.gitmodules b/.gitmodules index 39d1af9..9a5d4e4 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,6 +1,8 @@ [submodule "cwl-commandlinetools"] path = cwl-commandlinetools url = https://github.com/msk-access/cwl-commandlinetools.git + branch = hotfix/athena_inputs [submodule "cwl_subworkflows"] path = cwl_subworkflows url = https://github.com/msk-access/cwl_subworkflows.git + branch = hotfix/athena From 7a2552434a33b02d486246562173c083d44d90f0 Mon Sep 17 00:00:00 2001 From: buehlere Date: Tue, 16 May 2023 14:28:40 -0400 Subject: [PATCH 09/13] mismatching types --- qc_generator/nucleo_qc_generator.cwl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/qc_generator/nucleo_qc_generator.cwl b/qc_generator/nucleo_qc_generator.cwl index 4cc31d6..d33a9bd 100644 --- a/qc_generator/nucleo_qc_generator.cwl +++ b/qc_generator/nucleo_qc_generator.cwl @@ -192,7 +192,7 @@ inputs: 'sbg:x': 386.90625 'sbg:y': 2449.734375 - id: output - type: string? + type: 'string[]?' 'sbg:exposed': true - id: omaf type: boolean? From c2b3f8037d77962786cb20dc324419bef90954bb Mon Sep 17 00:00:00 2001 From: buehlere Date: Tue, 16 May 2023 16:10:41 -0400 Subject: [PATCH 10/13] updates --- cwl-commandlinetools | 2 +- cwl_subworkflows | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cwl-commandlinetools b/cwl-commandlinetools index b1f1494..0b0f7ab 160000 --- a/cwl-commandlinetools +++ b/cwl-commandlinetools @@ -1 +1 @@ -Subproject commit b1f149422fd0fdaa72be799e65643709920c2f44 +Subproject commit 0b0f7ab3b3ca148d7d208de82c317af009a6eaae diff --git a/cwl_subworkflows b/cwl_subworkflows index 39da215..e8d4cc3 160000 --- a/cwl_subworkflows +++ b/cwl_subworkflows @@ -1 +1 @@ -Subproject commit 39da2152220fa5b41f891b9187d08266906c729b +Subproject commit e8d4cc381d3009e57b23263c8b39dce73ff58f5b From 4fa958f3f644fa605e18e2dc606ab03f00f38868 Mon Sep 17 00:00:00 2001 From: buehlere Date: Tue, 16 May 2023 16:15:19 -0400 Subject: [PATCH 11/13] Update cwl_subworkflows --- cwl_subworkflows | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cwl_subworkflows b/cwl_subworkflows index e8d4cc3..e47443e 160000 --- a/cwl_subworkflows +++ b/cwl_subworkflows @@ -1 +1 @@ -Subproject commit e8d4cc381d3009e57b23263c8b39dce73ff58f5b +Subproject commit e47443e3734e3af14b199450b64f31036099ce23 From da61c7c163aeba4180e4099c79eabbfdf8a86406 Mon Sep 17 00:00:00 2001 From: buehlere Date: Wed, 17 May 2023 10:45:50 -0400 Subject: [PATCH 12/13] adding test for voyager toil --- requirements_voyager.txt | 7 +++++++ tox.ini | 11 +++++++++++ 2 files changed, 18 insertions(+) create mode 100644 requirements_voyager.txt diff --git a/requirements_voyager.txt b/requirements_voyager.txt new file mode 100644 index 0000000..bb8dd06 --- /dev/null +++ b/requirements_voyager.txt @@ -0,0 +1,7 @@ +coloredlogs==15.0.1 +pytest==7.2.0 +setuptools==65.4.1 +cwltool==3.1.20230425144158 +git+https://github.com/mskcc/toil.git@5.4.2#egg=toil[cwl] +pytest-runner==6.0.0 +tox==3.27.1 diff --git a/tox.ini b/tox.ini index 5022bb7..d7d5c97 100644 --- a/tox.ini +++ b/tox.ini @@ -22,3 +22,14 @@ passenv = {gh-actions,pytest} deps = -r ./requirements.txt # run the tests commands = pytest + +[testenv-voyager] + +passenv = {gh-actions,pytest} +# allowlist_externals= /bin/bash +# install data +# commands_pre = bash install_data.sh +# install testing framework +deps = -r ./requirements_voyager.txt +# run the tests +commands = pytest From 64685caff6a165a29573dee1429baa55faceb737 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Wed, 17 May 2023 19:07:17 -0400 Subject: [PATCH 13/13] Updating subworkflows --- cwl-commandlinetools | 2 +- cwl_subworkflows | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cwl-commandlinetools b/cwl-commandlinetools index 0b0f7ab..c8e3cad 160000 --- a/cwl-commandlinetools +++ b/cwl-commandlinetools @@ -1 +1 @@ -Subproject commit 0b0f7ab3b3ca148d7d208de82c317af009a6eaae +Subproject commit c8e3cad89655ab5675cd8bcfff97b1c0f8d8a1cd diff --git a/cwl_subworkflows b/cwl_subworkflows index e47443e..18a44c5 160000 --- a/cwl_subworkflows +++ b/cwl_subworkflows @@ -1 +1 @@ -Subproject commit e47443e3734e3af14b199450b64f31036099ce23 +Subproject commit 18a44c56e67d0202f565fbf9ac2ec07600e663e7