From 49b7689da256cbc57758abdd49c35b9acab5a769 Mon Sep 17 00:00:00 2001 From: Enis Afgan Date: Wed, 11 Sep 2024 16:35:01 -0400 Subject: [PATCH] [cloud] Update cloud toolbox (#836) --- cloud/assembly.yml | 2 ++ cloud/assembly.yml.lock | 9 +++++ cloud/bed.yml.lock | 3 +- cloud/collection_operations.yml | 2 ++ cloud/collection_operations.yml.lock | 8 +++++ cloud/convert_formats.yml.lock | 1 + cloud/datamash.yml.lock | 5 ++- cloud/deeptools.yml.lock | 16 +++++++++ cloud/expressiontools.yml.lock | 3 ++ cloud/fasta_fastq.yml.lock | 8 +++-- cloud/fastq_quality_control.yml.lock | 11 +++--- cloud/gemini.yml.lock | 7 ++-- cloud/get_data.yml.lock | 2 ++ cloud/graph_display_data.yml.lock | 4 +++ cloud/machine_learning.yml.lock | 2 +- cloud/mapping.yml.lock | 15 ++++++-- cloud/multiple_alignments.yml.lock | 6 ++++ cloud/nanopore.yml.lock | 7 ++++ cloud/pharmacology.yml.lock | 1 + cloud/picard.yml.lock | 3 +- cloud/qiime2.yml.lock | 5 +-- cloud/rna_seq.yml | 2 ++ cloud/rna_seq.yml.lock | 22 +++++++++--- cloud/sam_bam.yml.lock | 34 +++++++++++++++--- cloud/single_cell.yml | 3 ++ cloud/single_cell.yml.lock | 53 ++++++++++++++++++++++++---- cloud/text_manipulation.yml.lock | 19 +++++++--- cloud/variant_calling.yml.lock | 10 ++++-- cloud/vcf_bcf.yml.lock | 32 +++++++++++++++++ cloud/virology.yml.lock | 5 +++ 30 files changed, 261 insertions(+), 39 deletions(-) diff --git a/cloud/assembly.yml b/cloud/assembly.yml index ada06f50..dbc24e55 100644 --- a/cloud/assembly.yml +++ b/cloud/assembly.yml @@ -8,3 +8,5 @@ tools: owner: iuc - name: racon owner: bgruening +- name: gfastats + owner: bgruening diff --git a/cloud/assembly.yml.lock b/cloud/assembly.yml.lock index d0e8f50c..20a131ad 100644 --- a/cloud/assembly.yml.lock +++ b/cloud/assembly.yml.lock @@ -7,6 +7,7 @@ tools: owner: iuc revisions: - 9e3e80cc4ad4 + - e022dff952df tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: spades @@ -19,11 +20,19 @@ tools: owner: iuc revisions: - 8dee0218ac7d + - b799a615995d tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: racon owner: bgruening revisions: + - 78c533842eeb - a199cd7ac344 tool_panel_section_id: assembly tool_panel_section_label: Assembly +- name: gfastats + owner: bgruening + revisions: + - 3ef480892a9f + tool_panel_section_id: assembly + tool_panel_section_label: Assembly diff --git a/cloud/bed.yml.lock b/cloud/bed.yml.lock index 8b9fd2da..cbd678ee 100644 --- a/cloud/bed.yml.lock +++ b/cloud/bed.yml.lock @@ -6,7 +6,8 @@ tools: - name: bedtools owner: iuc revisions: - - ce3c7f062223 - 07e8b80f278c + - 64e2edfe7a2c + - ce3c7f062223 tool_panel_section_id: bed tool_panel_section_label: BED diff --git a/cloud/collection_operations.yml b/cloud/collection_operations.yml index d96d205c..b70976e7 100644 --- a/cloud/collection_operations.yml +++ b/cloud/collection_operations.yml @@ -8,3 +8,5 @@ tools: owner: iuc - name: collection_column_join owner: iuc +- name: pick_value + owner: iuc diff --git a/cloud/collection_operations.yml.lock b/cloud/collection_operations.yml.lock index e09fdcd8..6fed9d23 100644 --- a/cloud/collection_operations.yml.lock +++ b/cloud/collection_operations.yml.lock @@ -12,6 +12,7 @@ tools: - name: split_file_to_collection owner: bgruening revisions: + - 2dae863c8f42 - 6cbe2f30c2d7 tool_panel_section_id: collection_operations tool_panel_section_label: Collection Operations @@ -25,6 +26,13 @@ tools: owner: iuc revisions: - 071084070619 + - 3ddd99c7efee - 58228a4d58fe tool_panel_section_id: collection_operations tool_panel_section_label: Collection Operations +- name: pick_value + owner: iuc + revisions: + - b19e21af9c52 + tool_panel_section_id: collection_operations + tool_panel_section_label: Collection Operations diff --git a/cloud/convert_formats.yml.lock b/cloud/convert_formats.yml.lock index 5bd06e1b..ed96c9b4 100644 --- a/cloud/convert_formats.yml.lock +++ b/cloud/convert_formats.yml.lock @@ -7,4 +7,5 @@ tools: owner: iuc revisions: - b026dae67fba + tool_panel_section_id: convert_formats tool_panel_section_label: Convert Formats diff --git a/cloud/datamash.yml.lock b/cloud/datamash.yml.lock index 2a6310bf..5f1952a9 100644 --- a/cloud/datamash.yml.lock +++ b/cloud/datamash.yml.lock @@ -6,20 +6,23 @@ tools: - name: datamash_reverse owner: iuc revisions: + - b8a457820315 - f198773344e4 tool_panel_section_id: datamash tool_panel_section_label: Datamash - name: datamash_transpose owner: iuc revisions: + - 22c2a1ac7ae3 - 374cb875d38a + - a513e3fbb4c5 - ac092723240d - - 22c2a1ac7ae3 tool_panel_section_id: datamash tool_panel_section_label: Datamash - name: datamash_ops owner: iuc revisions: + - 4c07ddedc198 - 746e8e4bf929 tool_panel_section_id: datamash tool_panel_section_label: Datamash diff --git a/cloud/deeptools.yml.lock b/cloud/deeptools.yml.lock index b73919ce..674ae406 100644 --- a/cloud/deeptools.yml.lock +++ b/cloud/deeptools.yml.lock @@ -7,17 +7,20 @@ tools: owner: bgruening revisions: - 514fa53b5efb + - a60c359ec43c tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_plot_heatmap owner: bgruening revisions: - a4dfb122e52b + - e4c7985d4585 tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_bam_compare owner: bgruening revisions: + - c929a006727f - e821645ef8fc tool_panel_section_id: deeptools tool_panel_section_label: deepTools @@ -25,17 +28,20 @@ tools: owner: bgruening revisions: - 62eb6d63f582 + - c06951d10364 tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_bigwig_compare owner: bgruening revisions: + - 07418a30ed01 - 26e7304d6737 tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_compute_gc_bias owner: bgruening revisions: + - 26983857c91a - 2bc10a9ca58b tool_panel_section_id: deeptools tool_panel_section_label: deepTools @@ -43,17 +49,20 @@ tools: owner: bgruening revisions: - 2c37ce318bc3 + - e479c7ca5570 tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_multi_bam_summary owner: bgruening revisions: + - 01fb6a7654e6 - 78f405266706 tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_multi_bigwig_summary owner: bgruening revisions: + - 137c4beed34b - 3c9f0c486cca tool_panel_section_id: deeptools tool_panel_section_label: deepTools @@ -61,17 +70,20 @@ tools: owner: bgruening revisions: - 32e451def88c + - bad3ca889618 tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_plot_coverage owner: bgruening revisions: + - 231994413f89 - 56bce3c82278 tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_plot_enrichment owner: bgruening revisions: + - 4431f39ede55 - e65d16fb2724 tool_panel_section_id: deeptools tool_panel_section_label: deepTools @@ -79,23 +91,27 @@ tools: owner: bgruening revisions: - 2da482e408b8 + - 4ed32329e0ed tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_plot_pca owner: bgruening revisions: + - 443d9a9d6d11 - 69264da0ce77 tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_bam_coverage owner: bgruening revisions: + - 0e49b109abc2 - bb1e4f63e0e6 tool_panel_section_id: deeptools tool_panel_section_label: deepTools - name: deeptools_plot_profile owner: bgruening revisions: + - 6662b1a8d326 - c361b12d207a tool_panel_section_id: deeptools tool_panel_section_label: deepTools diff --git a/cloud/expressiontools.yml.lock b/cloud/expressiontools.yml.lock index 55f84f4b..c41eb420 100644 --- a/cloud/expressiontools.yml.lock +++ b/cloud/expressiontools.yml.lock @@ -6,10 +6,13 @@ tools: - name: map_param_value owner: iuc revisions: + - 5ac8a4bf7a8d - a01f088d0e5e + tool_panel_section_id: expression_tools tool_panel_section_label: Expression Tools - name: compose_text_param owner: iuc revisions: - e188c9826e0f + tool_panel_section_id: expression_tools tool_panel_section_label: Expression Tools diff --git a/cloud/fasta_fastq.yml.lock b/cloud/fasta_fastq.yml.lock index f27cd622..dcef0652 100644 --- a/cloud/fasta_fastq.yml.lock +++ b/cloud/fasta_fastq.yml.lock @@ -8,8 +8,10 @@ tools: revisions: - 093678460093 - 135b80fb1ac2 - - c5e2e5902201 + - 5eb7e84243f2 - 660cffd8d92a + - aa784cb3810d + - c5e2e5902201 tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ - name: fastq_filter @@ -51,6 +53,7 @@ tools: - name: flash owner: iuc revisions: + - 01a4ebf1f237 - a27654fc4270 tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ @@ -58,14 +61,15 @@ tools: owner: bgruening revisions: - 084bbd8ba7b8 + - cd7e644cae1d tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ - name: umi_tools_count owner: iuc revisions: - 8250ea3a1501 - - b557acca0b56 - a535cf1e5da4 + - b557acca0b56 tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ - name: umi_tools_extract diff --git a/cloud/fastq_quality_control.yml.lock b/cloud/fastq_quality_control.yml.lock index ee99a7bf..08e326da 100644 --- a/cloud/fastq_quality_control.yml.lock +++ b/cloud/fastq_quality_control.yml.lock @@ -6,27 +6,30 @@ tools: - name: multiqc owner: iuc revisions: + - 1c2db0054039 + - 5e33b465d8d5 - 75c93c70d094 - 9a913cdee30e - - df99138d2776 - abfd8a6544d7 - - 5e33b465d8d5 - - 1c2db0054039 + - df99138d2776 + - f7e2f1eb3a16 tool_panel_section_id: fastq_quality_control tool_panel_section_label: FASTQ Quality Control - name: fastp owner: iuc revisions: - 65b93b623c77 + - d60c3f704da0 - dbf9c561ef29 tool_panel_section_id: fastq_quality_control tool_panel_section_label: FASTQ Quality Control - name: fastqc owner: devteam revisions: + - 2c64fded1286 - 3d0c7bdf12f5 - - e7b2202befea - 9da02be9c6cc + - e7b2202befea tool_panel_section_id: fastq_quality_control tool_panel_section_label: FASTQ Quality Control - name: trimmomatic diff --git a/cloud/gemini.yml.lock b/cloud/gemini.yml.lock index efee7ba5..8d340131 100644 --- a/cloud/gemini.yml.lock +++ b/cloud/gemini.yml.lock @@ -8,16 +8,19 @@ tools: revisions: - 2270a8b83c12 - cf61daf064fe + tool_panel_section_id: gemini tool_panel_section_label: GEMINI - name: gemini_db_info owner: iuc revisions: - - c2a413e47fe9 - 4c5f4e9b1931 + - c2a413e47fe9 + tool_panel_section_id: gemini tool_panel_section_label: GEMINI - name: gemini_query owner: iuc revisions: - - 77a1e60fd1de - 666f60a9331a + - 77a1e60fd1de + tool_panel_section_id: gemini tool_panel_section_label: GEMINI diff --git a/cloud/get_data.yml.lock b/cloud/get_data.yml.lock index d406f524..4ef4cbb9 100644 --- a/cloud/get_data.yml.lock +++ b/cloud/get_data.yml.lock @@ -7,11 +7,13 @@ tools: owner: iuc revisions: - 83c7d564b128 + - 8848455c0270 tool_panel_section_id: get_data tool_panel_section_label: Get Data - name: ncbi_acc_download owner: iuc revisions: - 1c58de56d587 + - e063168e0a81 tool_panel_section_id: get_data tool_panel_section_label: Get Data diff --git a/cloud/graph_display_data.yml.lock b/cloud/graph_display_data.yml.lock index 9bb0af2a..0e251bf5 100644 --- a/cloud/graph_display_data.yml.lock +++ b/cloud/graph_display_data.yml.lock @@ -7,12 +7,14 @@ tools: owner: iuc revisions: - 2824d77cd8f8 + - 36b848d5f3ec tool_panel_section_id: graph_display_data tool_panel_section_label: Graph/Display Data - name: circos owner: iuc revisions: - df7356989ac1 + - c4bde687c846 tool_panel_section_id: graph_display_data tool_panel_section_label: Graph/Display Data - name: jbrowse @@ -27,6 +29,7 @@ tools: revisions: - 83c573f2e73c - 73b8cb5bddcd + - 2f557f6abbfb tool_panel_section_id: graph_display_data tool_panel_section_label: Graph/Display Data - name: pathview @@ -42,5 +45,6 @@ tools: - 53460afd5115 - 566197475670 - 4955e9bb96d1 + - 374e9062d874 tool_panel_section_id: graph_display_data tool_panel_section_label: Graph/Display Data diff --git a/cloud/machine_learning.yml.lock b/cloud/machine_learning.yml.lock index 3fb946e6..b66cd53a 100644 --- a/cloud/machine_learning.yml.lock +++ b/cloud/machine_learning.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: Machine Learning diff --git a/cloud/mapping.yml.lock b/cloud/mapping.yml.lock index 3ba7e81e..4c14c202 100644 --- a/cloud/mapping.yml.lock +++ b/cloud/mapping.yml.lock @@ -6,6 +6,7 @@ tools: - name: minimap2 owner: iuc revisions: + - 5cc34c3f440d - f54f5baedfdd tool_panel_section_id: mapping tool_panel_section_label: Mapping @@ -13,39 +14,47 @@ tools: owner: devteam revisions: - 09b2cdb7ace5 + - d5ceb9f3c25b tool_panel_section_id: mapping tool_panel_section_label: Mapping - name: bwa owner: devteam revisions: - - e188dc7a68e6 + - 2477830927ec - 3fe632431b68 + - e188dc7a68e6 tool_panel_section_id: mapping tool_panel_section_label: Mapping - name: bwameth owner: iuc revisions: - 29bdbc353f20 + - cf1322aeb137 tool_panel_section_id: mapping tool_panel_section_label: Mapping - name: lastz owner: devteam revisions: + - 37b497aa133f - e7f19d6a9af8 tool_panel_section_id: mapping tool_panel_section_label: Mapping - name: rgrnastar owner: iuc revisions: - - c772497b2c32 - 2055c2667eb3 + - 4014de1b6daf - 980d2a2e1180 + - b0f2be869d6d + - c772497b2c32 tool_panel_section_id: mapping tool_panel_section_label: Mapping - name: rna_starsolo owner: iuc revisions: - - eec9494fdafa + - 42ce70172b72 + - 45795f582ae9 - 79b885ce78d7 + - eec9494fdafa tool_panel_section_id: mapping tool_panel_section_label: Mapping diff --git a/cloud/multiple_alignments.yml.lock b/cloud/multiple_alignments.yml.lock index 94182b7f..f7483291 100644 --- a/cloud/multiple_alignments.yml.lock +++ b/cloud/multiple_alignments.yml.lock @@ -7,23 +7,27 @@ tools: owner: iuc revisions: - 636b049e6141 + - 7cd7a55a678d tool_panel_section_id: multiple_alignments tool_panel_section_label: Multiple Alignments - name: mummer_mummerplot owner: iuc revisions: - ebe3b0f84de9 + - fb43e8887350 tool_panel_section_id: multiple_alignments tool_panel_section_label: Multiple Alignments - name: mummer_show_coords owner: iuc revisions: - 959c1f8dae95 + - cf3c9489c088 tool_panel_section_id: multiple_alignments tool_panel_section_label: Multiple Alignments - name: mummer_dnadiff owner: iuc revisions: + - 5561a1193611 - 60698466facd tool_panel_section_id: multiple_alignments tool_panel_section_label: Multiple Alignments @@ -31,11 +35,13 @@ tools: owner: iuc revisions: - 48823c9635a4 + - 57f042937ba7 tool_panel_section_id: multiple_alignments tool_panel_section_label: Multiple Alignments - name: mummer_delta_filter owner: iuc revisions: - b3acbb3a6af0 + - e8fdceffea4c tool_panel_section_id: multiple_alignments tool_panel_section_label: Multiple Alignments diff --git a/cloud/nanopore.yml.lock b/cloud/nanopore.yml.lock index 06b8dfb5..2ca1df31 100644 --- a/cloud/nanopore.yml.lock +++ b/cloud/nanopore.yml.lock @@ -7,11 +7,13 @@ tools: owner: iuc revisions: - 43815fa60f3a + - eb746fa6f514 tool_panel_section_id: nanopore tool_panel_section_label: Nanopore - name: flye owner: bgruening revisions: + - 3e4f8642c77e - 3ee0ef312022 tool_panel_section_id: nanopore tool_panel_section_label: Nanopore @@ -19,23 +21,27 @@ tools: owner: iuc revisions: - a7228a7ea146 + - fc8804320156 tool_panel_section_id: nanopore tool_panel_section_label: Nanopore - name: medaka_variant_pipeline owner: iuc revisions: + - 1d62240feff3 - 336b3def9b2b tool_panel_section_id: nanopore tool_panel_section_label: Nanopore - name: medaka_consensus owner: iuc revisions: + - 18505fe2bdb1 - db25ec99c3ea tool_panel_section_id: nanopore tool_panel_section_label: Nanopore - name: nanoplot owner: iuc revisions: + - a38bdcec9e4c - edbb6c5028f5 tool_panel_section_id: nanopore tool_panel_section_label: Nanopore @@ -78,6 +84,7 @@ tools: - name: porechop owner: iuc revisions: + - 543cbeef3949 - 93d623d9979c tool_panel_section_id: nanopore tool_panel_section_label: Nanopore diff --git a/cloud/pharmacology.yml.lock b/cloud/pharmacology.yml.lock index 57068cd1..5708f4b6 100644 --- a/cloud/pharmacology.yml.lock +++ b/cloud/pharmacology.yml.lock @@ -6,6 +6,7 @@ tools: - name: pharmcat owner: bgruening revisions: + - 891283e0ee89 - d67642a21a1d tool_panel_section_id: pharmacology tool_panel_section_label: Pharmacology diff --git a/cloud/picard.yml.lock b/cloud/picard.yml.lock index 43de521c..920d02be 100644 --- a/cloud/picard.yml.lock +++ b/cloud/picard.yml.lock @@ -6,8 +6,9 @@ tools: - name: picard owner: devteam revisions: - - b502c227b5e6 + - 3f254c5ced1d - a1f0b3f4b781 + - b502c227b5e6 - b9fbec5ac6b2 tool_panel_section_id: picard tool_panel_section_label: Picard diff --git a/cloud/qiime2.yml.lock b/cloud/qiime2.yml.lock index 07ddd228..c8c3ecb2 100644 --- a/cloud/qiime2.yml.lock +++ b/cloud/qiime2.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tool_panel_section_label: QIIME2 @@ -7,4 +7,5 @@ tools: owner: q2d2 revisions: - 3f011fac899d - tool_panel_section_label: QIIME2 \ No newline at end of file + tool_panel_section_id: qiime2 + tool_panel_section_label: QIIME2 diff --git a/cloud/rna_seq.yml b/cloud/rna_seq.yml index 07a71a81..0035acc7 100644 --- a/cloud/rna_seq.yml +++ b/cloud/rna_seq.yml @@ -30,3 +30,5 @@ tools: owner: iuc - name: fgsea owner: iuc +- name: brew3r_r + owner: iuc diff --git a/cloud/rna_seq.yml.lock b/cloud/rna_seq.yml.lock index ff854f22..385b576b 100644 --- a/cloud/rna_seq.yml.lock +++ b/cloud/rna_seq.yml.lock @@ -7,40 +7,46 @@ tools: owner: bgruening revisions: - cc05793bb896 + - f4d5237a84f6 tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: kallisto_pseudo owner: iuc revisions: - 5ae5c312d718 + - ce5d418183c5 tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: kallisto_quant owner: iuc revisions: + - 4f9c4e6566e5 - 60f888039fb2 tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: deseq2 owner: iuc revisions: + - 6a3a025714d3 - 8fe98f7094de + - 9a882d108833 - cd9874cb9019 - - 6a3a025714d3 tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: limma_voom owner: iuc revisions: - 0921444c832d - - d6f5fa4ee473 + - 119b069fc845 - d5a940112511 + - d6f5fa4ee473 tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: edger owner: iuc revisions: - 334ce9b1bac5 + - ae2aad0a6d50 tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: sailfish @@ -53,22 +59,24 @@ tools: owner: iuc revisions: - 26371a1df031 - - f4af63aaf57a - 61ee47027bd3 + - f4af63aaf57a tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: stringtie owner: iuc revisions: - 1ebd14235b92 + - cbf488da3b2c tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: featurecounts owner: iuc revisions: + - 1759d845181e - 38b6d12edc68 - f3a5f075498f - - 1759d845181e + - f9d49f5cb597 tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq - name: cufflinks @@ -102,3 +110,9 @@ tools: - 17eb1e0d711f tool_panel_section_id: rna_seq tool_panel_section_label: RNA-seq +- name: brew3r_r + owner: iuc + revisions: + - 05f8e9d1e8b8 + tool_panel_section_id: rna_seq + tool_panel_section_label: RNA-seq diff --git a/cloud/sam_bam.yml.lock b/cloud/sam_bam.yml.lock index 2a0a9941..f4c81653 100644 --- a/cloud/sam_bam.yml.lock +++ b/cloud/sam_bam.yml.lock @@ -13,20 +13,24 @@ tools: owner: iuc revisions: - 19ece8afbaab + - 30a201c9c310 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_view owner: iuc revisions: - - 5826298f6a73 - 0dbf49c414ae + - 32dc5f781059 + - 5826298f6a73 - b72793637686 + - c370440f901e tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_reheader owner: devteam revisions: - 30388d878f81 + - 85e38b31e8b3 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: sam_pileup @@ -39,12 +43,14 @@ tools: owner: devteam revisions: - 4d343c1f606b + - 970e6333f07e tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: bamtools_split owner: devteam revisions: - 9676127a1ed2 + - 96c9315b0e29 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: sam2interval @@ -56,26 +62,29 @@ tools: - name: qualimap_multi_bamqc owner: iuc revisions: + - 17b35d23731f - e38af83df163 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_phase owner: devteam revisions: - - b5c3b1856370 - 1e5880498f52 + - b5c3b1856370 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_merge owner: iuc revisions: - - 740ce0a18f0d - 36677f429310 + - 740ce0a18f0d + - cae2794d2deb tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_markdup owner: iuc revisions: + - 40fa6c240105 - 83b8e36e9cbe - b5527cc104ab tool_panel_section_id: sam_bam @@ -84,18 +93,21 @@ tools: owner: iuc revisions: - bc0cc7bfbfe9 + - d2df79922531 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_fastx owner: iuc revisions: - a8d69aee190e + - b906586a6596 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_depth owner: iuc revisions: - 44de678a44c4 + - 971dc85e9441 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_stats @@ -103,17 +115,20 @@ tools: revisions: - 145f6d74ff5e - 24c5d43cb545 + - 541082d03bef tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_split owner: devteam revisions: - 135c85f4cfaf + - 818030fa6bbf tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_bedcov owner: devteam revisions: + - 6856f8a01905 - 9149ad20699a tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM @@ -121,6 +136,7 @@ tools: owner: devteam revisions: - 06dc50b7b711 + - 26b4f9f98aca tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_idxstats @@ -129,6 +145,7 @@ tools: - 7a6034296ae9 - 7def34e6cf4d - 811fc2d75ad4 + - fa5d3e61e429 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtool_filter2 @@ -141,37 +158,43 @@ tools: owner: devteam revisions: - 22970df7a40e + - fefd89ab563c tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_sort owner: devteam revisions: + - d54a4df48867 - e613c1ad4c4c tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_mpileup owner: devteam revisions: + - b61f5d6a7f25 - fa7ad9b89f4a tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: bam_to_sam owner: devteam revisions: + - 3c661e57a88f - 88eedb4abea0 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: bamtools_filter owner: devteam revisions: - - cb20f99fd45b - - bd735cae4ce6 - 108db6635177 + - 993b19f20c76 + - bd735cae4ce6 + - cb20f99fd45b tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: sam_to_bam owner: devteam revisions: + - 0e60e2dd20af - cf1ffd88f895 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM @@ -179,6 +202,7 @@ tools: owner: devteam revisions: - a4a10c7924d1 + - b8beef827165 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_rmdup diff --git a/cloud/single_cell.yml b/cloud/single_cell.yml index 11f96bfa..aceeb409 100644 --- a/cloud/single_cell.yml +++ b/cloud/single_cell.yml @@ -167,3 +167,6 @@ tools: - name: scanpy_plot_embed owner: ebi-gxa + + - name: cite_seq_count + owner: iuc diff --git a/cloud/single_cell.yml.lock b/cloud/single_cell.yml.lock index 9c72c162..a53e2df6 100644 --- a/cloud/single_cell.yml.lock +++ b/cloud/single_cell.yml.lock @@ -45,34 +45,39 @@ tools: owner: iuc revisions: - 55e35e9203cf + - 93dd15e13e6a - fb9e030ffae4 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: anndata_export owner: iuc revisions: - - 707023fa62fe - 0cb889db0910 + - 707023fa62fe + - e1c3c2f2a834 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: anndata_manipulate owner: iuc revisions: - - 9bd945a03d7b - 3d748954434b + - 9bd945a03d7b + - ed4996a16f7f tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: chromeister owner: iuc revisions: + - b768cc4cca40 - e483be1014b6 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: anndata_inspect owner: iuc revisions: - - 688357ad5e61 - 286a24ac079c + - 688357ad5e61 + - 6f0d0c784f09 - ee98d611afc6 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell @@ -80,13 +85,14 @@ tools: owner: iuc revisions: - 05631436cdf1 + - e98619de2776 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: dropletutils owner: iuc revisions: - - a9caad671439 - 2c1200fba922 + - a9caad671439 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: dropletutils_read_10x @@ -112,18 +118,21 @@ tools: revisions: - 2b0d3e2f402a - 41f34e925bd5 + - f3eb2291da05 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: raceid_filtnormconf owner: iuc revisions: - - c891d8b33ede - 43c146e25a43 + - b83fbc90161e + - c891d8b33ede tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: raceid_clustering owner: iuc revisions: + - 0bff0ee0683a - a4b734cd253b - f911a64454fb tool_panel_section_id: single_cell @@ -131,6 +140,7 @@ tools: - name: raceid_trajectory owner: iuc revisions: + - 2af7c5086a96 - 72979cac22b2 - c92d0f9338c5 tool_panel_section_id: single_cell @@ -138,6 +148,7 @@ tools: - name: raceid_inspecttrajectory owner: iuc revisions: + - a6821f856a1e - c8434a623268 - df8e4e54d367 tool_panel_section_id: single_cell @@ -146,6 +157,7 @@ tools: owner: bgruening revisions: - 04b494623f8e + - c9944a2600f1 - e4c01dcece8b tool_panel_section_id: single_cell tool_panel_section_label: Single-cell @@ -153,6 +165,7 @@ tools: owner: bgruening revisions: - 88c07fc4024c + - a896b8b7d264 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: slice_image @@ -211,42 +224,49 @@ tools: owner: iuc revisions: - aaa5da8e73a9 + - f9353ee6a0d4 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_filter owner: iuc revisions: + - 72a6bebab2a5 - b409c2486353 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_inspect owner: iuc revisions: + - c0a80a16560f - c5d3684f7c4c tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_normalize owner: iuc revisions: + - 9f354c7c8c92 - ab55fe8030b6 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_plot owner: iuc revisions: - - aa0c474463c2 + - 1072ce66b426 - a8f865950ac4 + - aa0c474463c2 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_remove_confounders owner: iuc revisions: + - a39040ae0a38 - bf2017df9837 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_read_10x owner: ebi-gxa revisions: + - 078aa23c9374 - c8391a25dee3 - d92e6f12b790 tool_panel_section_id: single_cell @@ -254,6 +274,7 @@ tools: - name: gtf2gene_list owner: ebi-gxa revisions: + - 14b3f2a4523b - 1a642de6db01 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell @@ -275,6 +296,7 @@ tools: revisions: - 54f1212d26ac - 6aa025ea64d3 + - a4774b7b2e85 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: retrieve_scxa @@ -287,6 +309,7 @@ tools: owner: ebi-gxa revisions: - 0387a2179f88 + - 73d43034c860 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_filter_cells @@ -294,6 +317,7 @@ tools: revisions: - 4c42e5d8cb7c - ba64b91ed2b9 + - bf1e0bdec1db tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_filter_genes @@ -301,11 +325,13 @@ tools: revisions: - 7857ea93a011 - a1698b43abeb + - cc64914b0cf4 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_normalise_data owner: ebi-gxa revisions: + - 3027cb62adbd - 439f7f939d46 - 463d4fa8f5ec tool_panel_section_id: single_cell @@ -315,11 +341,13 @@ tools: revisions: - 0edb75c411a4 - 5c62f39aab8f + - 64dd8bb151e1 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_scale_data owner: ebi-gxa revisions: + - 4cc9362782b4 - 9664a6c00fd1 - c6e52529260e tool_panel_section_id: single_cell @@ -327,6 +355,7 @@ tools: - name: scanpy_run_pca owner: ebi-gxa revisions: + - 4428dba93375 - 988edd5fa902 - ce93e630b55a tool_panel_section_id: single_cell @@ -334,6 +363,7 @@ tools: - name: scanpy_compute_graph owner: ebi-gxa revisions: + - 22bd5861706d - 2401808e20e8 - a58d4166805b tool_panel_section_id: single_cell @@ -343,6 +373,7 @@ tools: revisions: - 384cacc40611 - 8eff7ec034e3 + - abdb61e4afa3 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_run_umap @@ -350,18 +381,21 @@ tools: revisions: - 0f98603d0116 - abae3d11d920 + - ea91cfd0444e tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_find_cluster owner: ebi-gxa revisions: - 35caf3c27c91 + - 36735850e461 - 9e4f79e40b84 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_find_markers owner: ebi-gxa revisions: + - d8f5224005bb - eb01a7e59e9a - f04dd4e5b6a7 tool_panel_section_id: single_cell @@ -369,7 +403,14 @@ tools: - name: scanpy_plot_embed owner: ebi-gxa revisions: + - 7d5c97823f8b - 99dd7baf9e23 - a8ef4bc35839 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell +- name: cite_seq_count + owner: iuc + revisions: + - 3df3d1b51110 + tool_panel_section_label: single_cell + tool_panel_section_label: Single-cell diff --git a/cloud/text_manipulation.yml.lock b/cloud/text_manipulation.yml.lock index 4965bf71..6e062e29 100644 --- a/cloud/text_manipulation.yml.lock +++ b/cloud/text_manipulation.yml.lock @@ -7,34 +7,39 @@ tools: owner: iuc revisions: - 6544e4b87a4f + - 90f657745fea tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation - name: query_tabular owner: iuc revisions: - cf34c344508d + - cf4397560712 tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation - name: column_maker owner: devteam revisions: - - 6595517c2dd8 - 02026300aa45 + - 6595517c2dd8 + - aff5135563c6 tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation - name: sqlite_to_tabular owner: iuc revisions: - bce29ec10b78 + - c4d18aa4ec4a tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation - name: annotatemyids owner: iuc revisions: - 133f36c29579 + - 1a125daea0d8 - 44018dd6b447 + - a79ee60b6926 - fe3ca740a485 - - 1a125daea0d8 tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation - name: concatenate_multiple_datasets @@ -46,6 +51,7 @@ tools: - name: regex_find_replace owner: galaxyp revisions: + - 503bcd6ebe4b - ae8c4b2488e7 tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation @@ -60,6 +66,7 @@ tools: owner: bgruening revisions: - 37a53100b67e + - ff2a81aa3f08 tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation - name: add_input_name_as_column @@ -71,10 +78,12 @@ tools: - name: text_processing owner: bgruening revisions: + - 74a8bef53a00 + - 86755160afbf + - 9ff72e942410 - d698c222f354 - ddf54b12c295 - - 9ff72e942410 - - 74a8bef53a00 + - fbf99087e067 tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation - name: reshape2_melt @@ -99,11 +108,13 @@ tools: owner: iuc revisions: - 238981ed43b7 + - f7ad5e69aa60 tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation - name: column_remove_by_header owner: iuc revisions: + - 2040e4c2750a - 372967836e98 tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation diff --git a/cloud/variant_calling.yml.lock b/cloud/variant_calling.yml.lock index 9e7bd2eb..83175a2f 100644 --- a/cloud/variant_calling.yml.lock +++ b/cloud/variant_calling.yml.lock @@ -14,8 +14,8 @@ tools: owner: iuc revisions: - 4805fe3d8fda - - e1461b5c52a0 - 65432c3abf6c + - e1461b5c52a0 tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling - name: lofreq_viterbi @@ -28,6 +28,7 @@ tools: owner: iuc revisions: - 426d707dfc47 + - 971e07ca4456 tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling - name: lofreq_filter @@ -40,14 +41,15 @@ tools: owner: iuc revisions: - 09d6e4693887 + - 791f73caa0c8 tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling - name: freebayes owner: devteam revisions: + - 156b60c1530f - a5937157062f - ef2c525bd8cd - - 156b60c1530f tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling - name: snpsift_genesets @@ -66,15 +68,17 @@ tools: owner: iuc revisions: - 5b80f544c67f + - 68693743661e - 74aebe30fb52 + - 9473cd297a76 - cfcf33df7fc0 - - 68693743661e tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling - name: snpsift owner: iuc revisions: - 2e497a770bca + - 5fab4f81391d tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling - name: sniffles diff --git a/cloud/vcf_bcf.yml.lock b/cloud/vcf_bcf.yml.lock index eb159bac..a6ec035f 100644 --- a/cloud/vcf_bcf.yml.lock +++ b/cloud/vcf_bcf.yml.lock @@ -6,6 +6,7 @@ tools: - name: bcftools_consensus owner: iuc revisions: + - 8aa352093d73 - d6dc477167f8 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF @@ -13,35 +14,41 @@ tools: owner: iuc revisions: - 672b6c02fbc7 + - 7b4454382d39 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_plugin_fixploidy owner: iuc revisions: - '365325116147' + - dd72ff87cfd0 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_convert_to_vcf owner: iuc revisions: + - cfd81f17580b - fec517907949 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_norm owner: iuc revisions: + - 271965b55437 - c077f71d351f tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_query_list_samples owner: iuc revisions: + - 2c80b0d6bde0 - ed4ea9de1791 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_plugin_missing2ref owner: iuc revisions: + - 8b260d252ff4 - dfef7a353ed0 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF @@ -49,41 +56,48 @@ tools: owner: iuc revisions: - 01d6b7d6365e + - ccb83bf54de0 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_plugin_setgt owner: iuc revisions: - 8abfcd1a6949 + - a730269af659 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_plugin_counts owner: iuc revisions: - 4813f99d81b7 + - dadbd61dc4cf tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_mpileup owner: iuc revisions: + - 0a5dcc9a8ec2 - 0dbff46d5a1b tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_plugin_mendelian owner: iuc revisions: + - 8f5962c43868 - bf235558f2cf tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_concat owner: iuc revisions: + - 05f317e50e61 - d40d4bf05718 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_convert_from_vcf owner: iuc revisions: + - 012656fd329f - b8e9da766b0f tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF @@ -91,17 +105,20 @@ tools: owner: iuc revisions: - 776ad0b21536 + - bc5332d47b1c tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_reheader owner: iuc revisions: + - 2331ddcbd5aa - 9ef52d95114b tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_stats owner: iuc revisions: + - 591cc8518033 - b17394940c7a tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF @@ -109,11 +126,13 @@ tools: owner: iuc revisions: - 582f8b13873d + - a12844ca467a tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_plugin_fill_tags owner: iuc revisions: + - b10d1510fa84 - bf7d6acd9884 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF @@ -121,11 +140,13 @@ tools: owner: iuc revisions: - 02f349bdbf96 + - 39bca000353d tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_merge owner: iuc revisions: + - 5b006286a458 - e03f2f3ac3a9 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF @@ -133,53 +154,62 @@ tools: owner: iuc revisions: - b76adb2f1c51 + - fa65af07ce7d tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_call owner: iuc revisions: - 072f606e2e69 + - 07396b423218 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_view owner: iuc revisions: + - 1a2ef636f48e - 23680a42e149 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_filter owner: iuc revisions: + - 46fcafba49ec - 6ca7c55a27e8 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_csq owner: iuc revisions: + - d237eaef451f - fdd127bd4a32 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_annotate owner: iuc revisions: + - 2c372041ed8c - 403553ae19f6 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_plugin_dosage owner: iuc revisions: + - 283911fe7e1a - 5c232a738c74 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_query owner: iuc revisions: + - 31a1b89eab9b - c9c5718edc19 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: bcftools_plugin_tag2tag owner: iuc revisions: + - 3897eaadfbff - bdfdf5f6e950 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF @@ -230,6 +260,7 @@ tools: owner: devteam revisions: - 2968c6916579 + - aa8e8c96ca06 tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF - name: vcfcombine @@ -295,6 +326,7 @@ tools: - name: vcfsort owner: devteam revisions: + - dd44c3f416c3 - f0580efedada tool_panel_section_id: vcf_bcf tool_panel_section_label: VCF/BCF diff --git a/cloud/virology.yml.lock b/cloud/virology.yml.lock index 100ab31c..4c1b77f4 100644 --- a/cloud/virology.yml.lock +++ b/cloud/virology.yml.lock @@ -6,12 +6,14 @@ tools: - name: ivar_trim owner: iuc revisions: + - a250929be21b - db536ad45f28 tool_panel_section_id: virology tool_panel_section_label: Virology - name: ivar_removereads owner: iuc revisions: + - 5dc33613c288 - ee2beb764a7b tool_panel_section_id: virology tool_panel_section_label: Virology @@ -24,6 +26,7 @@ tools: - name: ivar_consensus owner: iuc revisions: + - 3a72fede57ce - 78bbd17d0703 tool_panel_section_id: virology tool_panel_section_label: Virology @@ -31,6 +34,7 @@ tools: owner: iuc revisions: - 7fe36019c073 + - fcbeda41d0ac tool_panel_section_id: virology tool_panel_section_label: Virology - name: ivar_getmasked @@ -42,6 +46,7 @@ tools: - name: ivar_variants owner: iuc revisions: + - abbc8041e8ec - f95f403841ad tool_panel_section_id: virology tool_panel_section_label: Virology