diff --git a/conf/modules.config b/conf/modules.config index e8e3e63..40b2dbc 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -55,6 +55,7 @@ process { } withName: SPACERANGER_COUNT { + ext.args = '--create-bam false' publishDir = [ path: { "${params.outdir}/${meta.id}/spaceranger" }, mode: params.publish_dir_mode, diff --git a/modules.json b/modules.json index 86c77ee..e071f8c 100644 --- a/modules.json +++ b/modules.json @@ -23,7 +23,7 @@ }, "spaceranger/count": { "branch": "master", - "git_sha": "3bd057bfdfb64578636ff3ae7f7cb8eeab3c0cb6", + "git_sha": "2f0ef0cd414ea43e33625023c72b6af936dce63d", "installed_by": ["modules"] }, "untar": { diff --git a/modules/nf-core/spaceranger/count/main.nf b/modules/nf-core/spaceranger/count/main.nf index cac83e0..4f766cb 100644 --- a/modules/nf-core/spaceranger/count/main.nf +++ b/modules/nf-core/spaceranger/count/main.nf @@ -2,7 +2,7 @@ process SPACERANGER_COUNT { tag "$meta.id" label 'process_high' - container "docker.io/nfcore/spaceranger:2.1.0" + container "nf-core/spaceranger:3.0.0" input: tuple val(meta), path(reads), path(image), path(cytaimage), path(darkimage), path(colorizedimage), path(alignment), path(slidefile) diff --git a/modules/nf-core/spaceranger/count/tests/main.nf.test b/modules/nf-core/spaceranger/count/tests/main.nf.test index b751b07..7631d85 100644 --- a/modules/nf-core/spaceranger/count/tests/main.nf.test +++ b/modules/nf-core/spaceranger/count/tests/main.nf.test @@ -2,6 +2,7 @@ nextflow_process { name "Test Process SPACERANGER_COUNT" script "../main.nf" + config "./nextflow.config" process "SPACERANGER_COUNT" tag "modules" @@ -210,7 +211,8 @@ nextflow_process { 'molecule_info.h5', 'barcodes.tsv.gz', 'features.tsv.gz', - 'matrix.mtx.gz' + 'matrix.mtx.gz', + 'cloupe.cloupe' ]} ).match() }, diff --git a/modules/nf-core/spaceranger/count/tests/main.nf.test.snap b/modules/nf-core/spaceranger/count/tests/main.nf.test.snap index ece665f..c13496e 100644 --- a/modules/nf-core/spaceranger/count/tests/main.nf.test.snap +++ b/modules/nf-core/spaceranger/count/tests/main.nf.test.snap @@ -2,53 +2,89 @@ "spaceranger v1 (stub) - homo_sapiens - fasta - gtf - fastq - tif - csv": { "content": [ [ - "versions.yml:md5,038e17e049a72dd3d417d0e221dce732" + "versions.yml:md5,1539e8a9a3d63ce3653920721d1af509" ] ], - "timestamp": "2024-01-09T15:09:24.723008" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-02T09:29:02.205153668" }, "spaceranger v2 - homo_sapiens - fasta - gtf - fastq - tif - csv": { "content": [ [ - "versions.yml:md5,038e17e049a72dd3d417d0e221dce732" + "versions.yml:md5,1539e8a9a3d63ce3653920721d1af509" ], [ - "filtered_feature_bc_matrix.h5:md5,509e18ed6b218850e5095124ecc771c1", - "metrics_summary.csv:md5,412caff0fcd9f39cb54671147058de2f", - "possorted_genome_bam.bam:md5,23cd192fcc217d835b8c0afee0619f40", - "possorted_genome_bam.bam.bai:md5,baf623d3e554ba5008304f32414c9fb2", + "clusters.csv:md5,2cc2d0c94ec0af69f03db235f9ea6932", + "clusters.csv:md5,46c12f3845e28f27f2cd580cb004c0ea", + "clusters.csv:md5,4e5f082240b9c9903168842d1f9dbe34", + "clusters.csv:md5,e626eb7049baf591ea49f5d8c305621c", + "clusters.csv:md5,65cfb24fc937e4df903a742c1adf8b08", + "clusters.csv:md5,819a71787618945dacfa2d5301b953b1", + "clusters.csv:md5,5ae17ed02cdb9f61d7ceb0cd6922c9d4", + "clusters.csv:md5,641550bec22e02fff3611087f7fd6e07", + "clusters.csv:md5,9fbe5c79035175bc1899e9a7fc80f7ac", + "clusters.csv:md5,ed0c2dcca15c14a9983407ff9af0daaf", + "differential_expression.csv:md5,d37a8ef21699372ec4a4bdf0c43d71b7", + "differential_expression.csv:md5,ac3181524385c88d38a0fc17d3bdd526", + "differential_expression.csv:md5,557d6dfec7421c392aa6443725608cd1", + "differential_expression.csv:md5,1437fad68d701c97a4a46318aee45575", + "differential_expression.csv:md5,7a2f3d0e90782055580f4903617a7d27", + "differential_expression.csv:md5,41756e9570d07aee6aed710e6a965846", + "differential_expression.csv:md5,62ea7651c3f195d3c960c6c688dca477", + "differential_expression.csv:md5,b630542266c4abb71f4205922340498d", + "differential_expression.csv:md5,0deb97f0be7e72ad73e456092db31e6d", + "differential_expression.csv:md5,3bba8490f753507e7e2e29be759f218b", + "components.csv:md5,568bb9bcb6ee913356fcb4be3fea1911", + "dispersion.csv:md5,e2037b1db404f6e5d8b3144629f2500d", + "features_selected.csv:md5,3ba6d1315ae594963b306d94ba1180e7", + "projection.csv:md5,aef5d71381678d5245e471f3d5a8ab67", + "variance.csv:md5,475a95e51ce66e639ae21d801c455e2b", + "projection.csv:md5,928c0f68a9c773fba590941d3d5af7ca", + "projection.csv:md5,216dcc5589a083fcc27d981aa90fa2ab", + "filtered_feature_bc_matrix.h5:md5,f1a8f225c113974b47efffe08e70f367", + "metrics_summary.csv:md5,faa17487b479eab361050d3266da2efb", "probe_set.csv:md5,5bfb8f12319be1b2b6c14142537c3804", - "raw_feature_bc_matrix.h5:md5,2263d2c756785f86dc28f6b76fd61b73", + "raw_feature_bc_matrix.h5:md5,6e40ae93a116c6fc0adbe707b0eb415f", "raw_probe_bc_matrix.h5:md5,3d5e711d0891ca2caaf301a2c1fbda91", "aligned_fiducials.jpg:md5,51dcc3a32d3d5ca4704f664c8ede81ef", "cytassist_image.tiff:md5,0fb04a55e5658f4d158d986a334b034d", - "detected_tissue_image.jpg:md5,64d9adb4844ab91506131476d93b28dc", - "tissue_hires_image.png:md5,1c0f1e94522a886c19f56a629227e097", + "detected_tissue_image.jpg:md5,1d3ccc1e12c4fee091b006e48b9cc16a", + "spatial_enrichment.csv:md5,1117792553e82feb2b4b3934907a0136", + "tissue_hires_image.png:md5,834706fff299024fab48e6366afc9cb9", "tissue_lowres_image.png:md5,8c1fcb378f7f886301f49ffc4f84360a", - "tissue_positions.csv:md5,1b2df34f9e762e9e64aa226226b96c4b" + "tissue_positions.csv:md5,425601ef21661ec0126000f905ef044f" ] ], - "timestamp": "2024-01-11T17:49:27.776247" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-02T10:13:00.787792273" }, "spaceranger v1 - homo_sapiens - fasta - gtf - fastq - tif - csv": { "content": [ [ - "versions.yml:md5,038e17e049a72dd3d417d0e221dce732" + "versions.yml:md5,1539e8a9a3d63ce3653920721d1af509" ], [ - "filtered_feature_bc_matrix.h5:md5,f444a4816bf40d377271a6157b320556", - "metrics_summary.csv:md5,5e36f2f9b6987791e0b5eb2736d25115", - "molecule_info.h5:md5,b3d14dfbfc167bb8fc9b158f083efdb6", - "possorted_genome_bam.bam:md5,6ed7f3bb2f17322113f940989a3771ff", - "possorted_genome_bam.bam.bai:md5,08ce9ffd30d9b82091932b744873610b", - "raw_feature_bc_matrix.h5:md5,7e937b4863a98b0d3784f4e21c07c326", + "filtered_feature_bc_matrix.h5:md5,7e09d1cd2e1f497a698c5efde9e4af84", + "metrics_summary.csv:md5,07a6fcc2e20f854f8d3fcde2457a2f9a", + "molecule_info.h5:md5,1f2e0fd31d15509e7916e84f22632c9c", + "raw_feature_bc_matrix.h5:md5,5a4184a3bfaf722eec8d1a763a45906e", "aligned_fiducials.jpg:md5,f6217ddd707bb189e665f56b130c3da8", - "detected_tissue_image.jpg:md5,4a26b91db5aca179d627b86f352006e2", + "detected_tissue_image.jpg:md5,c1c7e8741701a576c1ec103c1aaf98ea", "tissue_hires_image.png:md5,d91f8f176ae35ab824ede87117ac0889", "tissue_lowres_image.png:md5,475a04208d193191c84d7a3b5d4eb287", - "tissue_positions.csv:md5,37d288d0e29e8572ea4c5bef292de4b6" + "tissue_positions.csv:md5,748bf590c445db409d7dbdf5a08e72e8" ] ], - "timestamp": "2024-01-11T20:34:18.669838" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-02T09:37:13.128424153" } } \ No newline at end of file diff --git a/modules/nf-core/spaceranger/count/tests/nextflow.config b/modules/nf-core/spaceranger/count/tests/nextflow.config new file mode 100644 index 0000000..fe9d61a --- /dev/null +++ b/modules/nf-core/spaceranger/count/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: SPACERANGER_COUNT { + ext.args = '--create-bam false' + } +} diff --git a/tests/pipeline/test_downstream.nf.test.snap b/tests/pipeline/test_downstream.nf.test.snap index 824113d..c848af7 100644 --- a/tests/pipeline/test_downstream.nf.test.snap +++ b/tests/pipeline/test_downstream.nf.test.snap @@ -9,4 +9,4 @@ }, "timestamp": "2024-03-19T18:46:59.035976" } -} +} \ No newline at end of file diff --git a/tests/pipeline/test_spaceranger_ffpe_v1.nf.test.snap b/tests/pipeline/test_spaceranger_ffpe_v1.nf.test.snap index 063d565..ee3d586 100644 --- a/tests/pipeline/test_spaceranger_ffpe_v1.nf.test.snap +++ b/tests/pipeline/test_spaceranger_ffpe_v1.nf.test.snap @@ -11,12 +11,12 @@ }, "nf_core_pipeline_software_mqc_versions.yml": { "content": [ - "{CLUSTERING={quarto=1.3.450, papermill=null}, FASTQC={fastqc=0.12.1}, QUALITY_CONTROLS={quarto=1.3.450, papermill=null}, READ_DATA={scanpy=1.9.8}, SPACERANGER_COUNT={spaceranger=2.1.0}, SPACERANGER_UNTAR_REFERENCE={untar=1.3}, SPATIALLY_VARIABLE_GENES={quarto=1.3.450, papermill=null}, UNTAR_SPACERANGER_INPUT={untar=1.3}, Workflow={nf-core/spatialtranscriptomics=v1.0dev}}" + "{CLUSTERING={quarto=1.3.450, papermill=null}, FASTQC={fastqc=0.12.1}, QUALITY_CONTROLS={quarto=1.3.450, papermill=null}, READ_DATA={scanpy=1.9.8}, SPACERANGER_COUNT={spaceranger=3.0.0}, SPACERANGER_UNTAR_REFERENCE={untar=1.3}, SPATIALLY_VARIABLE_GENES={quarto=1.3.450, papermill=null}, UNTAR_SPACERANGER_INPUT={untar=1.3}, Workflow={nf-core/spatialtranscriptomics=v1.0dev}}" ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.02.0" }, - "timestamp": "2024-03-19T18:31:18.231368" + "timestamp": "2024-04-04T10:08:16.975105" } -} +} \ No newline at end of file diff --git a/tests/pipeline/test_spaceranger_ffpe_v2_cytassist.nf.test.snap b/tests/pipeline/test_spaceranger_ffpe_v2_cytassist.nf.test.snap index 032f4ef..92e16a3 100644 --- a/tests/pipeline/test_spaceranger_ffpe_v2_cytassist.nf.test.snap +++ b/tests/pipeline/test_spaceranger_ffpe_v2_cytassist.nf.test.snap @@ -1,12 +1,12 @@ { "nf_core_pipeline_software_mqc_versions.yml": { "content": [ - "{CLUSTERING={quarto=1.3.450, papermill=null}, FASTQC={fastqc=0.12.1}, QUALITY_CONTROLS={quarto=1.3.450, papermill=null}, READ_DATA={scanpy=1.9.8}, SPACERANGER_COUNT={spaceranger=2.1.0}, SPACERANGER_UNTAR_REFERENCE={untar=1.3}, SPATIALLY_VARIABLE_GENES={quarto=1.3.450, papermill=null}, UNTAR_SPACERANGER_INPUT={untar=1.3}, Workflow={nf-core/spatialtranscriptomics=v1.0dev}}" + "{CLUSTERING={quarto=1.3.450, papermill=null}, FASTQC={fastqc=0.12.1}, QUALITY_CONTROLS={quarto=1.3.450, papermill=null}, READ_DATA={scanpy=1.9.8}, SPACERANGER_COUNT={spaceranger=3.0.0}, SPACERANGER_UNTAR_REFERENCE={untar=1.3}, SPATIALLY_VARIABLE_GENES={quarto=1.3.450, papermill=null}, UNTAR_SPACERANGER_INPUT={untar=1.3}, Workflow={nf-core/spatialtranscriptomics=v1.0dev}}" ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.02.0" }, - "timestamp": "2024-03-19T18:45:01.126974" + "timestamp": "2024-04-04T10:42:54.76102" } -} +} \ No newline at end of file