Update README to reflect availability of docker

adamd3 · Oct 9, 2023 · 54ed310 · 54ed310
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diff --git a/README.md b/README.md
@@ -42,22 +42,22 @@ Mandatory arguments:
   --ref_ann [file]                Path to GFF file containing reference genome annotation.
   --sample_file [file]            Path to file containing sample information.
   -profile [str]                  Configuration profile to use.
-                                  Available: conda (coming soon: docker, singularity).
+                                  Available: conda, docker, singularity.
 
 Other options:
   --aligner [str]                 (Pseudo-)aligner to be used. Options: `bwa`, `kallisto`. Default = bwa.
   --cont_tabl [file]              Path to tsv file containing contrasts to be performed for differential expression.
   --fragment_len [str]            Estimated average fragment length for kallisto transcript quantification (only required for single-end reads). Default = 150.
   --fragment_sd [str]             Estimated standard deviation of fragment length for kallisto transcript quantification (only required for single-end reads). Default = 20.
-  --func_file [file]              Path to GMT-format file containing functional annotation.
+  --func_file [file]              Path to GFF3-format file containing functional annotations.
   --l2fc_thresh [str]             Absolute log2(FoldChange) threshold for identifying differentially expressed genes. Default = 1.
   --outdir [file]                 The output directory where the results will be saved (Default: './results').
   --paired [str]                  Data are paired-end.
   --p_thresh [str]                Adjusted p-value threshold for identifying differentially expressed genes. Default = 0.05.
   --skip_trimming [bool]          Do not trim adaptors from FastQ files.
   --strandedness [str]            Is data stranded? Options: `unstranded`, `forward`, `reverse`. Default = reverse.
   -name [str]                     Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic.
-
+  -resume:                        Re-start the pipeline if it has been previously run.
 ```
 
 Explanation of parameters:
@@ -74,7 +74,6 @@ Explanation of parameters:
 - `l2fc_thresh`: absolute log2(FoldChange) threshold for identifying differentially expressed genes. Default = 1.
 - `skip_trimming`: do not trim adaptors from reads.
 - `outdir`: the output directory where the results will be saved (Default: `./results`).
-- `-resume`: will re-start the pipeline if it has been previously run.
 
 ## Required inputs
 
@@ -127,7 +126,7 @@ Explanation of parameters:
   ```
 
 - **Functional annotation file**: CSV file containing functional categories for genes. Enrichment testing will be performed
-  on results from differential gene expression contrasts. First column contains the gene ID (must match the gene IDs in `locus_tag` of the GFF annotation file); second column contains the functional groups (e.g. GO terms, but can be any functional categories).
+  on results from differential gene expression contrasts. First column contains the gene ID (must match the gene IDs in `locus_tag` of the GFF annotation file); second column contains the functional groups (GO terms).
 
   Example:
 

diff --git a/main.nf b/main.nf
@@ -295,29 +295,30 @@ workflow.onComplete {
 def helpMessage() {
     log.info"""
     Usage:
-    nextflow run BactSeq --data_dir [dir] --sample_file [file] --ref_genome [file] --ref_ann [file] -profile docker [other_options]
+    nextflow run BactSeq --data_dir [dir] --sample_file [file] --ref_genome [file] --ref_ann [file] -profile conda [other_options]
 
     Mandatory arguments:
-      --data_dir [file]               Path to directory containing FastQ files.
-      --ref_genome [file]             Path to FASTA file containing reference genome sequence (bwa) or multi-FASTA file containing coding gene sequences (kallisto).
-      --ref_ann [file]                Path to GFF file containing reference genome annotation.
-      --sample_file [file]            Path to file containing sample information.
-      -profile [str]                  Configuration profile to use.
-                                      Available: conda, docker, singularity.
+    --data_dir [file]               Path to directory containing FastQ files.
+    --ref_genome [file]             Path to FASTA file containing reference genome sequence (bwa) or multi-FASTA file containing coding gene sequences (kallisto).
+    --ref_ann [file]                Path to GFF file containing reference genome annotation.
+    --sample_file [file]            Path to file containing sample information.
+    -profile [str]                  Configuration profile to use.
+                                    Available: conda, docker, singularity.
 
     Other options:
-      --aligner [str]                 (Pseudo-)aligner to be used. Options: `bwa`, `kallisto`. Default = bwa.
-      --cont_tabl [file]              Path to tsv file containing contrasts to be performed for differential expression.
-      --fragment_len [str]            Estimated average fragment length for kallisto transcript quantification (only required for single-end reads). Default = 150.
-      --fragment_sd [str]             Estimated standard deviation of fragment length for kallisto transcript quantification (only required for single-end reads). Default = 20.
-      --func_file [file]              Path to GMT-format file containing functional annotation.
-      --l2fc_thresh [str]             Absolute log2(FoldChange) threshold for identifying differentially expressed genes. Default = 1.
-      --outdir [file]                 The output directory where the results will be saved (Default: './results').
-      --paired [str]                  Data are paired-end.     
-      --p_thresh [str]                Adjusted p-value threshold for identifying differentially expressed genes. Default = 0.05.
-      --skip_trimming [bool]          Do not trim adaptors from FastQ files.
-      --strandedness [str]            Is data stranded? Options: `unstranded`, `forward`, `reverse`. Default = reverse.
-      -name [str]                     Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic.
+    --aligner [str]                 (Pseudo-)aligner to be used. Options: `bwa`, `kallisto`. Default = bwa.
+    --cont_tabl [file]              Path to tsv file containing contrasts to be performed for differential expression.
+    --fragment_len [str]            Estimated average fragment length for kallisto transcript quantification (only required for single-end reads). Default = 150.
+    --fragment_sd [str]             Estimated standard deviation of fragment length for kallisto transcript quantification (only required for single-end reads). Default = 20.
+    --func_file [file]              Path to GFF3-format file containing functional annotations.
+    --l2fc_thresh [str]             Absolute log2(FoldChange) threshold for identifying differentially expressed genes. Default = 1.
+    --outdir [file]                 The output directory where the results will be saved (Default: './results').
+    --paired [str]                  Data are paired-end.
+    --p_thresh [str]                Adjusted p-value threshold for identifying differentially expressed genes. Default = 0.05.
+    --skip_trimming [bool]          Do not trim adaptors from FastQ files.
+    --strandedness [str]            Is data stranded? Options: `unstranded`, `forward`, `reverse`. Default = reverse.
+    -name [str]                     Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic.
+    -resume:                        Re-start the pipeline if it has been previously run.
 
     """.stripIndent()
 }