Nextflow Modules
Showing module(s) with keyword "cram"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/ascat | Process | bam copy number cram | copy number profiles of tumour cells. |
| nf-core/bam_applybqsr | Workflow | bam cram bqsr recalibration gatk4 | Apply Base Quality Score Recalibration (BQSR) to a BAM or CRAM file using GATK4 ApplyBQSR. Supports scatter-gather across genomic intervals: when more than one interval file is supplied per sample, the interval-level outputs are merged back together with samtools merge. When no intervals are supplied (num_intervals: 0), ApplyBQSR is run once on the whole input and no merge step is performed. |
| nf-core/bam_cnv_wisecondorx | Workflow | cnv bam bed cram plots genomics | A subworkflow for calling CNVs using WisecondorX |
| nf-core/bam_dedup_stats_samtools_umicollapse | Workflow | umi dedup index bam sam cram | umicollapse, index BAM file and run samtools stats, flagstat and idxstats |
| nf-core/bam_dedup_stats_samtools_umitools | Workflow | umi dedup index bam sam cram | UMI-tools dedup, index BAM file and run samtools stats, flagstat and idxstats |
| nf-core/bam_impute_quilt2 | Workflow | bam cram imputation quilt quilt2 vcf | Impute low-coverage BAM or CRAM inputs with QUILT2 and ligate chunked outputs per chromosome. "regionout", "regionoutPadded", "regionSize" keys will be added to the meta map to distinguish the different files before ligation and therefore should not be used. |
| nf-core/bam_markduplicates_picard | Workflow | markduplicates bam sam cram | Picard MarkDuplicates, index BAM file and run samtools stats, flagstat and idxstats |
| nf-core/bam_markduplicates_samtools | Workflow | markdup bam sam cram | Samtools markduplicate SAM/BAM/CRAM file |
| nf-core/bam_qc_picard | Workflow | statistics counts hs_metrics wgs_metrics bam sam cram | Produces comprehensive statistics from BAM file |
| nf-core/bam_sort_stats_samtools | Workflow | sort bam sam cram | Sort SAM/BAM/CRAM file |
| nf-core/bam_split_by_region | Workflow | split bam sam cram index | Split the reads in the input bam by specified genomic region. |
| nf-core/bam_stats_samtools | Workflow | statistics counts bam sam cram | Produces comprehensive statistics from SAM/BAM/CRAM file |
| nf-core/bam_subsampledepth_samtools | Workflow | subsample bam sam cram | Subsample a BAM/CRAM/SAM file using samtools to a given mean depth. "region", "subsample_fraction", "mean_depth" and "depth" keys will be added to the meta map to distinguish the different file generated and therefore shouldn't be used. The `depth` key will be added to the meta map of the output channel. |
| nf-core/bam_telomere_estimation | Workflow | telomere telseq telogator2 telomerehunter bam cram | Estimate telomere length and content from aligned reads using telseq, telogator2, and telomerehunter |
| nf-core/bam_variant_calling_sort_freebayes_bcftools | Workflow | variant sort index bam cram vcf | Call variants using freebayes, then sort and index |
| nf-core/bam_variant_demix_boot_freyja | Workflow | bam variants cram | Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference) |
| nf-core/biobambam/bammarkduplicates2 | Process | markduplicates bam cram | Locate and tag duplicate reads in a BAM file |