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APipe Tester edited this page Dec 27, 2022
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| CWL | Description | Docker Requirement |
|---|---|---|
| add_strelka_gt.cwl | add GT tags | ubuntu:bionic |
| add_string_at_line.cwl | Insert an arbitrary string at a specific line of a file | ubuntu:xenial |
| add_string_at_line_bgzipped.cwl | Insert an arbitrary string at a specific line of a gzipped file | quay.io/biocontainers/samtools:1.11--h6270b1f_0 |
| add_vep_fields_to_table.cwl | add VEP annotation to report | griffithlab/vatools:4.1.0 |
| agfusion.cwl | A tool that annotates STAR gene fusion predictions | mgibio/agfusion:1.3.1-ensembl-95 |
| align_and_tag.cwl | align with bwa_mem and tag | mgibio/alignment_helper-cwl:1.0.0 |
| aligned_seq_fda_stats.cwl | mgibio/cle:v1.4.2 | |
| annotsv.cwl | mgibio/annotsv-cwl:2.1 | |
| annotsv_filter.cwl | filter AnnotSV tsv output generated from a bcftools merged vcf | python:3 |
| apply_bqsr.cwl | apply BQSR | broadinstitute/gatk:4.1.8.1 |
| bam_readcount.cwl | run bam-readcount | mgibio/bam_readcount_helper-cwl:1.1.1 |
| bam_to_bigwig.cwl | cgpBigWig Converting BAM to BigWig | quay.io/biocontainers/cgpbigwig:1.4.0--h93d22ca_0 |
| bam_to_cram.cwl | BAM to CRAM conversion | quay.io/biocontainers/samtools:1.11--h6270b1f_0 |
| bam_to_fastq.cwl | Picard: BAM to FASTQ | mgibio/rnaseq:1.0.0 |
| bam_to_sam.cwl | BAM to SAM conversion | quay.io/biocontainers/samtools:1.11--h6270b1f_0 |
| bcftools_merge.cwl | mgibio/bcftools-cwl:1.12 | |
| bedgraph_to_bigwig.cwl | bedGraph to bigwig conversion | mgibio/bisulfite:v1.4 |
| bedtools_intersect.cwl | quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0 | |
| bgzip.cwl | bgzip VCF | quay.io/biocontainers/samtools:1.11--h6270b1f_0 |
| biscuit_align.cwl | Biscuit: align | mgibio/biscuit:0.3.8 |
| biscuit_markdup.cwl | Biscuit dedup | mgibio/biscuit:0.3.8 |
| biscuit_pileup.cwl | Biscuit pileup | mgibio/biscuit:0.3.8 |
| bisulfite_qc_conversion.cwl | Biscuit QC: Bisulfite conversion rate. | mgibio/biscuit:0.3.8.2 |
| bisulfite_qc_coverage_stats.cwl | Biscuit QC: Bisulfite conversion rate. | mgibio/biscuit:0.3.8.2 |
| bisulfite_qc_cpg_retention_distribution.cwl | Biscuit QC: CpG Retention Distribution | mgibio/biscuit:0.3.8.2 |
| bisulfite_qc_mapping_summary.cwl | Biscuit QC: Bisulfite conversion rate. | mgibio/biscuit:0.3.8.2 |
| bisulfite_vcf2bed.cwl | convert a biscuit pileup vcf to a bed and bedgraph file, via a wrapper script | mgibio/biscuit:0.3.8 |
| bqsr.cwl | create BQSR table | broadinstitute/gatk:4.1.8.1 |
| call_duplex_consensus.cwl | call duplex consensus | quay.io/biocontainers/fgbio:1.3.0--0 |
| call_molecular_consensus.cwl | call molecular consensus | quay.io/biocontainers/fgbio:1.3.0--0 |
| cat_all.cwl | ubuntu:xenial | |
| cat_out.cwl | ubuntu:xenial | |
| cellmatch_lineage.cwl | Running a script to identify lineage of cells | mgibio/scrna_lineage_inference:0.2 |
| cellranger_atac_count.cwl | Run Cell Ranger ATAC Count | registry.gsc.wustl.edu/mgi/cellranger-atac:1.0.1 |
| cellranger_count.cwl | Run Cell Ranger Count | registry.gsc.wustl.edu/alex.paul/cellranger:6.0.0 |
| cellranger_feature_barcoding.cwl | Run Cell Ranger Count with feature barcoding | registry.gsc.wustl.edu/alex.paul/cellranger:6.0.0 |
| cellranger_mkfastq.cwl | Run Cell Ranger mkfastq | registry.gsc.wustl.edu/alex.paul/cellranger:6.0.0 |
| cellranger_vdj.cwl | Run Cell Ranger V(D)J | registry.gsc.wustl.edu/alex.paul/cellranger:6.0.0 |
| cle_aml_trio_report_alignment_stat.cwl | cle aml_trio alignment_stat report | mgibio/cle-aml-trio-reports:v1.0 |
| cle_aml_trio_report_coverage_stat.cwl | cle aml_trio hs_metrics coverage_stat report | mgibio/cle-aml-trio-reports:v1.0 |
| cle_aml_trio_report_full_variants.cwl | cle aml_trio full variants report | mgibio/cle-aml-trio-reports:v1.0 |
| clip_overlap.cwl | clip overlapping reads | quay.io/biocontainers/fgbio:1.3.0--0 |
| cnvkit_batch.cwl | etal/cnvkit:0.9.8 | |
| cnvkit_vcf_export.cwl | Convert default cnvkit .cns output to standard vcf format | etal/cnvkit:0.9.5 |
| cnvnator.cwl | Run CNVnator to calculate copy number variations in WGS samples | mgibio/cnvnator-cwl:0.4 |
| collect_alignment_summary_metrics.cwl | collect alignment summary metrics | broadinstitute/picard:2.23.6 |
| collect_gc_bias_metrics.cwl | collect gc bias metrics | broadinstitute/picard:2.23.6 |
| collect_hs_metrics.cwl | collect HS metrics | broadinstitute/picard:2.23.6 |
| collect_insert_size_metrics.cwl | collect insert size metrics | broadinstitute/picard:2.23.6 |
| collect_wgs_metrics.cwl | collect WGS metrics | broadinstitute/picard:2.23.6 |
| combine_gvcfs.cwl | GATK CombineGVCFs | broadinstitute/gatk:4.1.8.1 |
| combine_variants.cwl | CombineVariants (GATK 3.6) | mgibio/gatk-cwl:3.6.0 |
| combine_variants_concordance.cwl | CombineVariants (GATK 3.6) | mgibio/gatk-cwl:3.6.0 |
| combine_variants_wgs.cwl | CombineVariants (GATK 3.6) | mgibio/gatk-cwl:3.6.0 |
| concordance.cwl | Concordance checking between Tumor and Normal BAM | brentp/somalier:v0.1.5 |
| cram_to_bam.cwl | samtools view cram to bam | quay.io/biocontainers/samtools:1.11--h6270b1f_0 |
| docm_add_variants.cwl | CombineVariants (GATK 3.6) | mgibio/gatk-cwl:3.6.0 |
| docm_gatk_haplotype_caller.cwl | HaplotypeCaller (GATK4) | broadinstitute/gatk:4.1.2.0 |
| downsample.cwl | downsample unaligned BAM | broadinstitute/gatk:4.1.4.1 |
| duphold.cwl | mgibio/duphold-cwl:0.1.5 | |
| duplex_seq_metrics.cwl | collect duplex seq metrics | quay.io/biocontainers/fgbio:1.3.0--0 |
| eval_cle_gold.cwl | Make CLE gold evaluation output and vaf report | ubuntu:bionic |
| eval_vaf_report.cwl | Generate vaf report for concordance analysis | ubuntu:bionic |
| extract_hla_alleles.cwl | ubuntu:xenial | |
| extract_umis.cwl | extract umis from bam | quay.io/biocontainers/fgbio:1.3.0--0 |
| fastq_to_bam.cwl | fastq to bam | mgibio/dna-alignment:1.0.0 |
| fastqc.cwl | Report metrics on bam or fastq files using fastqc | mgibio/fastqc:0.11.9 |
| filter_consensus.cwl | filter consensus reads | quay.io/biocontainers/fgbio:1.3.0--0 |
| filter_known_variants.cwl | Adds an INFO tag (VALIDATED) flagging variants in the pipeline vcf present in a previously validated vcf file | mgibio/bcftools-cwl:1.12 |
| filter_sv_vcf_blocklist_bedpe.cwl | mgibio/basespace_chromoseq:v12 | |
| filter_sv_vcf_depth.cwl | mgibio/bcftools-cwl:1.12 | |
| filter_sv_vcf_read_support.cwl | mgibio/bcftools-cwl:1.12 | |
| filter_sv_vcf_size.cwl | mgibio/bcftools-cwl:1.12 | |
| filter_vcf_cle.cwl | cle_annotated_vcf_filter | mgibio/cle:v1.3.1 |
| filter_vcf_coding_variant.cwl | Coding Variant filter | mgibio/vep_helper-cwl:vep_101.0_v1 |
| filter_vcf_custom_allele_freq.cwl | Custom allele frequency filter | mgibio/vep_helper-cwl:vep_101.0_v1 |
| filter_vcf_depth.cwl | filter variants at sites below a given sequence depth in each sample | mgibio/depth-filter:0.1.2 |
| filter_vcf_docm.cwl | Filter variants from the DoCM detector | mgibio/cle:v1.4.2 |
| filter_vcf_mapq0.cwl | filter vcf for variants with high percentage of mapq0 reads | mgibio/mapq0-filter:v0.5.4 |
| filter_vcf_somatic_llr.cwl | use the binomial/llr somatic filter to weed out low confidence variants | mgibio/somatic-llr-filter:v0.4.3 |
| fix_vcf_header.cwl | fix vcf header | broadinstitute/picard:2.23.6 |
| fp_filter.cwl | False Positive filter | mgibio/fp_filter-cwl:1.0.1 |
| gather_to_sub_directory.cwl | ubuntu:xenial | |
| gatherer.cwl | ubuntu:xenial | |
| gatk_genotypegvcfs.cwl | GATK GenotypeGVCFs | broadinstitute/gatk:4.1.8.1 |
| gatk_haplotype_caller.cwl | GATK HaplotypeCaller | broadinstitute/gatk:4.1.8.1 |
| generate_fda_tables.cwl | Script to create FDA-requested summary tables | python:3.7.4-slim-buster |
| generate_qc_metrics.cwl | Picard: RNA Seq Metrics | mgibio/rnaseq:1.0.0 |
| germline_combine_variants.cwl | CombineVariants (GATK 3.6) | mgibio/gatk-cwl:3.6.0 |
| grolar.cwl | grolar- pizzly gene fusion output parser | mgibio/grolar-cwl:1.0 |
| group_reads.cwl | group reads by umi | quay.io/biocontainers/fgbio:1.3.0--0 |
| hisat2_align.cwl | HISAT2: align | mgibio/hisat2-sambamba:0.1 |
| hla_consensus.cwl | Script to create consensus from optitype and clinical HLA typing | python:3.7.4-slim-buster |
| homer_tag_directory.cwl | Creating the homer tag directory | mgibio/homer:4.11.1 |
| index_bam.cwl | samtools index | quay.io/biocontainers/samtools:1.11--h6270b1f_0 |
| index_cram.cwl | samtools index cram | quay.io/biocontainers/samtools:1.11--h6270b1f_0 |
| index_vcf.cwl | vcf index | quay.io/biocontainers/samtools:1.11--h6270b1f_0 |
| intersect_known_variants.cwl | Intersect passing validated variants and passing pipeline variants for use in pvacseq | mgibio/bcftools-cwl:1.12 |
| interval_list_expand.cwl | expand interval list regions by a given number of basepairs | broadinstitute/picard:2.23.6 |
| intervals_to_bed.cwl | ubuntu:bionic | |
| kallisto.cwl | Kallisto: Quant | quay.io/biocontainers/kallisto:0.46.1--h4f7b962_0 |
| kmer_size_from_index.cwl | Helper script to pull the k-mer size used in generating a kallisto index from the index file | ubuntu:bionic |
| manta_somatic.cwl | Set up and execute manta | mgibio/manta_somatic-cwl:1.6.0 |
| mark_duplicates_and_sort.cwl | Mark duplicates and Sort | mgibio/mark_duplicates-cwl:1.0.1 |
| mark_illumina_adapters.cwl | fastq to bam | mgibio/dna-alignment:1.0.0 |
| md5sum.cwl | ubuntu:bionic | |
| merge_bams.cwl | Sambamba: merge | mgibio/bam-merge:0.1 |
| merge_bams_samtools.cwl | Samtools: merge | quay.io/biocontainers/samtools:0.1.19--hfb9b9cc_8 |
| merge_vcf.cwl | vcf merge | mgibio/bcftools-cwl:1.12 |
| mutect.cwl | Mutect2 (GATK 4) | broadinstitute/gatk:4.2.3.0 |
| name_sort.cwl | sort BAM by name | mgibio/sambamba-cwl:0.6.4 |
| normalize_variants.cwl | Normalize variants | broadinstitute/gatk:4.1.8.1 |
| optitype_dna.cwl | Run optitype on dna samples | mgibio/immuno_tools-cwl:1.0.1 |
| picard_merge_vcfs.cwl | Picard MergeVcfs | broadinstitute/gatk:4.1.8.1 |
| pindel.cwl | pindel v0.2.5b8 | mgibio/cle:v1.4.2 |
| pindel2vcf.cwl | pindel v0.2.5b8 | mgibio/cle:v1.3.1 |
| pindel_somatic_filter.cwl | pindel somatic filter v1 | mgibio/cle:v1.3.1 |
| pizzly.cwl | pizzly gene fusion detector | mgibio/pizzly-cwl:0.37.3 |
| pvacbind.cwl | run pVACbind | griffithlab/pvactools:3.1.1 |
| pvacfuse.cwl | run pVACfuse | griffithlab/pvactools:3.1.1 |
| pvacseq.cwl | run pVACseq | griffithlab/pvactools:3.1.1 |
| pvacseq_combine_variants.cwl | Combine germline and somatic vcf for pVACseq phasing | mgibio/gatk-cwl:3.6.0 |
| pvacvector.cwl | run pVACvector | griffithlab/pvactools:3.1.1 |
| read_backed_phasing.cwl | Read-backed phasing | mgibio/gatk-cwl:3.6.0 |
| realign.cwl | umi realignment | mgibio/dna-alignment:1.0.0 |
| remove_end_tags.cwl | remove END INFO tags | mgibio/bcftools-cwl:1.12 |
| rename.cwl | Renamer | |
| rename_for_staging.cwl | Rename file paths with identical basenames so that output staging works | python:3.7.4-slim-buster |
| replace_vcf_sample_name.cwl | mgibio/bcftools-cwl:1.12 | |
| samtools_flagstat.cwl | samtools flagstat | quay.io/biocontainers/samtools:1.11--h6270b1f_0 |
| samtools_sort.cwl | samtools sort | quay.io/biocontainers/samtools:1.11--h6270b1f_0 |
| select_variants.cwl | SelectVariants (GATK 4.1.8.1) | broadinstitute/gatk:4.1.8.1 |
| sequence_align_and_tag.cwl | align with bwa_mem and tag | mgibio/alignment_helper-cwl:1.1.0 |
| sequence_to_bam.cwl | resolve sequence type to a bam | broadinstitute/picard:2.23.6 |
| sequence_to_fastq.cwl | Picard: BAM to FASTQ | broadinstitute/picard:2.23.6 |
| set_filter_status.cwl | create filtered VCF | mgibio/gatk-cwl:3.6.0 |
| single_sample_docm_filter.cwl | docm filter | mgibio/perl_helper-cwl:1.0.0 |
| smoove.cwl | Run Smoove v0.2.7 | brentp/smoove:v0.2.7 |
| somatic_concordance_graph.cwl | Generate somatic concordance report graph | registry.gsc.wustl.edu/mgi-cle/somatic-concordance-report:v1 |
| sompy.cwl | som.py compares variants in vcf by location and alleles (using bcftools isec). | pkrusche/hap.py:v0.3.9 |
| sort_vcf.cwl | Sort VCF | broadinstitute/picard:2.23.6 |
| split_interval_list.cwl | broadinstitute/picard:2.24.2 | |
| split_interval_list_to_bed.cwl | mgibio/cle:v1.4.2 | |
| staged_rename.cwl | Staged Renamer | ubuntu:bionic |
| star_align_fusion.cwl | STAR: align reads to transcriptome | trinityctat/starfusion:1.10.1 |
| star_fusion_detect.cwl | STAR-Fusion identify candidate fusion transcript | trinityctat/starfusion:1.10.1 |
| strandedness_check.cwl | runs how_are_we_stranded_here to determine RNAseq data strandedness | mgibio/checkstrandedness:v1 |
| strelka.cwl | strelka 2.9.9 | mgibio/strelka-cwl:2.9.9 |
| stringtie.cwl | StringTie | quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0 |
| survivor.cwl | Run SURVIVOR to merge SV calls | mgibio/survivor-cwl:1.0.6.2 |
| transcript_to_gene.cwl | Kallisto: TranscriptToGene | mgibio/rnaseq:1.0.0 |
| trim_fastq.cwl | Trim FASTQ (flexbar) | mgibio/bisulfite:v1.4 |
| umi_align.cwl | umi alignment | mgibio/dna-alignment:1.0.0 |
| unaligned_seq_fda_stats.cwl | mgibio/cle:v1.4.2 | |
| variants_to_table.cwl | SelectVariants (GATK 4.1.8.1) | broadinstitute/gatk:4.1.8.1 |
| varscan_germline.cwl | varscan v2.4.2 germline | mgibio/varscan_helper-cwl:1.0.0 |
| varscan_process_somatic.cwl | varscan v2.4.2 processSomatic | mgibio/cle:v1.3.1 |
| varscan_somatic.cwl | varscan v2.4.2 somatic | mgibio/cle:v1.3.1 |
| vcf_expression_annotator.cwl | add expression info to vcf | griffithlab/vatools:4.1.0 |
| vcf_readcount_annotator.cwl | add bam_readcount info to vcf | griffithlab/vatools:4.1.0 |
| vcf_sanitize.cwl | Sanitize a VCF | mgibio/samtools-cwl:1.0.0 |
| vep.cwl | Ensembl Variant Effect Predictor | mgibio/vep_helper-cwl:vep_101.0_v2 |
| verify_bam_id.cwl | verify BAM ID | mgibio/verify_bam_id-cwl:1.1.3 |
| vt_decompose.cwl | run vt decompose | quay.io/biocontainers/vt:0.57721--hf74b74d_1 |
| xenosplit.cwl | Xenosplit | mgibio/xenosplit:0.5 |