From 56853f52323ce23538c99c4c7bbb073d377a6459 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 27 Nov 2023 10:02:52 +0000 Subject: [PATCH 1/2] Address @mashehu feedback for release --- docs/usage.md | 6 +++--- nextflow_schema.json | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 32cac7cf..2250c9a8 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -27,7 +27,7 @@ This may well be the same sample sheet used to generate the input matrix. For ex For example: -```console +```csv sample,fastq_1,fastq_2,condition,replicate,batch CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,control,1,A CONTROL_REP2,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz,control,2,B @@ -80,7 +80,7 @@ To use this approach, include the transcript lengths file with the **raw counts* Without the transcript lengths, for instance in earlier rnaseq workflow versions, follow the second recommendation in the [tximport documentation](https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#Downstream_DGE_in_Bioconductor): -> "Use the tximport argument countsFromAbundance='lengthScaledTPM' or 'scaledTPM', then employ the gene-level count matrix txi$counts directly in downstream software, a method we call 'bias corrected counts without an offset'" +> "Use the tximport argument `countsFromAbundance='lengthScaledTPM'` or `'scaledTPM'`, then employ the gene-level count matrix `txi$counts` directly in downstream software, a method we call 'bias corrected counts without an offset'" This aligns with the **gene_counts_length_scaled.tsv** or **gene_counts_scaled.tsv** matrices in the rnaseq workflow. @@ -130,7 +130,7 @@ Full list of features metadata are available on GEO platform pages. The contrasts file references the observations file to define groups of samples to compare. For example, based on the sample sheet above we could define contrasts like: -```console +```csv id,variable,reference,target,blocking condition_control_treated,condition,control,treated, condition_control_treated_blockrep,condition,control,treated,replicate;batch diff --git a/nextflow_schema.json b/nextflow_schema.json index 442b7d0e..3011e2c9 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -79,8 +79,8 @@ "transcript_length_matrix": { "type": "string", "fa_icon": "fas fa-border-all", - "description": "(RNA-seq only): optional transcript length matrix with sample samples and genes as the abundance matrix", - "help_text": "if provided, this file willl be used to provide transcript lengths to DESeq2 to model lengh bias across samples" + "description": "(RNA-seq only): optional transcript length matrix with samples and genes as the abundance matrix", + "help_text": "if provided, this file willl be used to provide transcript lengths to DESeq2 to model length bias across samples" }, "affy_cel_files_archive": { "type": "string", @@ -359,7 +359,7 @@ "exploratory_n_features": { "type": "integer", "default": 500, - "description": "Number of features selected before certain exploratory analyses. If -1, will use all features", + "description": "Number of features selected before certain exploratory analyses. If -1, will use all features.", "fa_icon": "fas fa-list-ol" }, "exploratory_whisker_distance": { From 2341fbd20974b0959eae4ea393fbcb20f053ef4a Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 27 Nov 2023 10:04:50 +0000 Subject: [PATCH 2/2] Poke CI --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index 2250c9a8..8365799d 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -84,7 +84,7 @@ Without the transcript lengths, for instance in earlier rnaseq workflow versions This aligns with the **gene_counts_length_scaled.tsv** or **gene_counts_scaled.tsv** matrices in the rnaseq workflow. -Important to note, the documentation advises: +It is important to note that the documentation advises: > "Do not manually pass the original gene-level counts to downstream methods without an offset."