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remove spaces in {{ ref_genome file }} in docs

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Chris Wright 2025-03-04 16:24:06 +00:00
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3 changed files with 6 additions and 6 deletions
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4
README.md
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@ -233,8 +233,8 @@ Output files may be aggregated including information for all samples or provided
| Transcript counts filtered | de_analysis/filtered_transcript_counts_with_genes.tsv | Filtered transcript counts, used for differential transcript usage analysis. Includes a reference to the associated gene ID. | aggregated | | Transcript counts filtered | de_analysis/filtered_transcript_counts_with_genes.tsv | Filtered transcript counts, used for differential transcript usage analysis. Includes a reference to the associated gene ID. | aggregated |
| Transcript info table | {{ alias }}_transcripts_table.tsv | This file details each isoform that was reconstructed from the input reads. It contains a subset of columns from the .tmap output from [gffcompare](https://ccb.jhu.edu/software/stringtie/gffcompare.shtml) | per-sample | | Transcript info table | {{ alias }}_transcripts_table.tsv | This file details each isoform that was reconstructed from the input reads. It contains a subset of columns from the .tmap output from [gffcompare](https://ccb.jhu.edu/software/stringtie/gffcompare.shtml) | per-sample |
| Final non redundant transcriptome | de_analysis/final_non_redundant_transcriptome.fasta | Transcripts that were used for differential expression analysis including novel transcripts with the identifiers used for DE analysis. Only applicable when the ref_transcriptome parameter is not provided. | aggregated | | Final non redundant transcriptome | de_analysis/final_non_redundant_transcriptome.fasta | Transcripts that were used for differential expression analysis including novel transcripts with the identifiers used for DE analysis. Only applicable when the ref_transcriptome parameter is not provided. | aggregated |
| Index of reference FASTA file | igv_reference/{{ ref_genome file }}.fai | Reference genome index of the FASTA file required for IGV config. | aggregated | | Index of reference FASTA file | igv_reference/{{ ref_genome_file }}.fai | Reference genome index of the FASTA file required for IGV config. | aggregated |
| GZI index of the reference FASTA file | igv_reference/{{ ref_genome file }}.gzi | GZI Index of the reference FASTA file. | aggregated | | GZI index of the reference FASTA file | igv_reference/{{ ref_genome_file }}.gzi | GZI Index of the reference FASTA file. | aggregated |
| JSON configuration file for IGV browser | igv.json | JSON configuration file to be loaded in IGV for visualising alignments against the reference. | aggregated | | JSON configuration file for IGV browser | igv.json | JSON configuration file to be loaded in IGV for visualising alignments against the reference. | aggregated |
| BAM file (minimap2) | BAMS/{{ alias }}.reads_aln_sorted.bam | BAM file generated from mapping input reads to the reference. | per-sample | | BAM file (minimap2) | BAMS/{{ alias }}.reads_aln_sorted.bam | BAM file generated from mapping input reads to the reference. | per-sample |
| BAM index file (minimap2) | BAMS/{{ alias }}.reads_aln_sort.bam.bai | Index file generated from mapping input reads to the reference. | per-sample | | BAM index file (minimap2) | BAMS/{{ alias }}.reads_aln_sort.bam.bai | Index file generated from mapping input reads to the reference. | per-sample |

4
docs/07_outputs.md
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@ -26,8 +26,8 @@ Output files may be aggregated including information for all samples or provided
| Transcript counts filtered | de_analysis/filtered_transcript_counts_with_genes.tsv | Filtered transcript counts, used for differential transcript usage analysis. Includes a reference to the associated gene ID. | aggregated | | Transcript counts filtered | de_analysis/filtered_transcript_counts_with_genes.tsv | Filtered transcript counts, used for differential transcript usage analysis. Includes a reference to the associated gene ID. | aggregated |
| Transcript info table | {{ alias }}_transcripts_table.tsv | This file details each isoform that was reconstructed from the input reads. It contains a subset of columns from the .tmap output from [gffcompare](https://ccb.jhu.edu/software/stringtie/gffcompare.shtml) | per-sample | | Transcript info table | {{ alias }}_transcripts_table.tsv | This file details each isoform that was reconstructed from the input reads. It contains a subset of columns from the .tmap output from [gffcompare](https://ccb.jhu.edu/software/stringtie/gffcompare.shtml) | per-sample |
| Final non redundant transcriptome | de_analysis/final_non_redundant_transcriptome.fasta | Transcripts that were used for differential expression analysis including novel transcripts with the identifiers used for DE analysis. Only applicable when the ref_transcriptome parameter is not provided. | aggregated | | Final non redundant transcriptome | de_analysis/final_non_redundant_transcriptome.fasta | Transcripts that were used for differential expression analysis including novel transcripts with the identifiers used for DE analysis. Only applicable when the ref_transcriptome parameter is not provided. | aggregated |
| Index of reference FASTA file | igv_reference/{{ ref_genome file }}.fai | Reference genome index of the FASTA file required for IGV config. | aggregated | | Index of reference FASTA file | igv_reference/{{ ref_genome_file }}.fai | Reference genome index of the FASTA file required for IGV config. | aggregated |
| GZI index of the reference FASTA file | igv_reference/{{ ref_genome file }}.gzi | GZI Index of the reference FASTA file. | aggregated | | GZI index of the reference FASTA file | igv_reference/{{ ref_genome_file }}.gzi | GZI Index of the reference FASTA file. | aggregated |
| JSON configuration file for IGV browser | igv.json | JSON configuration file to be loaded in IGV for visualising alignments against the reference. | aggregated | | JSON configuration file for IGV browser | igv.json | JSON configuration file to be loaded in IGV for visualising alignments against the reference. | aggregated |
| BAM file (minimap2) | BAMS/{{ alias }}.reads_aln_sorted.bam | BAM file generated from mapping input reads to the reference. | per-sample | | BAM file (minimap2) | BAMS/{{ alias }}.reads_aln_sorted.bam | BAM file generated from mapping input reads to the reference. | per-sample |
| BAM index file (minimap2) | BAMS/{{ alias }}.reads_aln_sort.bam.bai | Index file generated from mapping input reads to the reference. | per-sample | | BAM index file (minimap2) | BAMS/{{ alias }}.reads_aln_sort.bam.bai | Index file generated from mapping input reads to the reference. | per-sample |

4
output_definition.json
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@ -193,7 +193,7 @@
"type": "aggregated" "type": "aggregated"
}, },
"reference-index": { "reference-index": {
"filepath": "igv_reference/{{ ref_genome file }}.fai", "filepath": "igv_reference/{{ ref_genome_file }}.fai",
"title": "Index of reference FASTA file", "title": "Index of reference FASTA file",
"description": "Reference genome index of the FASTA file required for IGV config.", "description": "Reference genome index of the FASTA file required for IGV config.",
"mime-type": "text/tab-separated-values", "mime-type": "text/tab-separated-values",
@ -201,7 +201,7 @@
"type": "aggregated" "type": "aggregated"
}, },
"reference-gzi-index": { "reference-gzi-index": {
"filepath": "igv_reference/{{ ref_genome file }}.gzi", "filepath": "igv_reference/{{ ref_genome_file }}.gzi",
"title": "GZI index of the reference FASTA file", "title": "GZI index of the reference FASTA file",
"description": "GZI Index of the reference FASTA file.", "description": "GZI Index of the reference FASTA file.",
"mime-type": "application/octet-stream", "mime-type": "application/octet-stream",