Merge branch 'dev' of https://github.com/nf-core/airrflow into dev

nf-core · Mar 10, 2023 · 704bb07 · 704bb07
2 parents d843f74 + 604ef8a
commit 704bb07
Showing 15 changed files with 46 additions and 46 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -34,7 +34,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 | presto     | 0.7.0       | 0.7.1       |
 | changeo    | 1.2.0       | 1.3.0       |
 | igblast    | 1.17.1      | 1.19.0      |
-| r-enchantr |             | 0.1.0       |
+| r-enchantr |             | 0.1.1       |
 | r-plotly   |             | 4.10.1      |
 
 ### `Deprecated`

diff --git a/assets/repertoire_comparison.Rmd b/assets/repertoire_comparison.Rmd
@@ -53,12 +53,12 @@ dir.create(seq_dir)
 ## Sequence assembly steps
 
 Number of reads for each of the samples and number of sequences left after performing sequence assembly and alignment to reference data.
-The full table can be found under [Table_sequences_assembly]("./Sequence_numbers_summary/Table_sequences_assembly.tsv").
+The full table can be found under [Table_sequences_assembly](repertoire_comparison/Sequence_numbers_summary/Table_sequences_assembly.tsv).
 
 ```{r seq_numbers, echo=FALSE, warning=FALSE, results='asis'}
 read_table <- function(tab_file){
         tab_seqs <- read.table(tab_file, header=TRUE, sep="\t", check.names = FALSE)
-        #write.table(tab_seqs, file=paste0(seq_dir,"/Table_sequences_assembly.tsv"), sep="\t", quote=F, row.names=F)
+        write.table(tab_seqs, file=paste0(seq_dir,"/Table_sequences_assembly.tsv"), sep="\t", quote=F, row.names=F)
     }
 tryCatch( {read_table("./Table_sequences.tsv")} ,
   error=function(e){message("No sequence numbers are available if starting with assembled reads.")}
@@ -97,7 +97,7 @@ tryCatch( {
 ## Filtering and clonal analysis steps
 
 Number of sequences for each of the samples after each of the downstream filtering and clonal analysis steps.
-The full table can be found under [Table_sequences_assembled]("./Sequence_numbers_summary/Table_sequences_assembled.tsv").
+The full table can be found under [Table_sequences_assembled](repertoire_comparison/Sequence_numbers_summary/Table_sequences_assembled.tsv).
 
 ```{r seq_assembled, echo=FALSE, warning=FALSE, results='asis'}
 tab_seqs_assembled <- read.table("./Table_sequences_assembled.tsv", header=TRUE, sep="\t", check.names = FALSE)
@@ -114,8 +114,8 @@ dat <- dat %>% dplyr::relocate(any_of(c("sample_id","ConvertDb-fasta", "AssignGe
                                 "ParseDb-split", "FilterJunctionMod3","AddMetadata","SingleCellQC","CreateGermlines",
                                 "RemoveChimeric","CollapseDuplicates","ClonePass"))) %>% dplyr::arrange(sample_id)
 
-
-#write.table(dat, file=paste0(seq_dir,"/Table_sequences_assembled.tsv"), sep="\t", quote=F, row.names=F)
+dat <- apply(dat,2,as.character)
+write.table(dat, file=paste0(seq_dir,"/Table_sequences_assembled.tsv"), sep="\t", quote=F, row.names=F)
 ```
 
 
@@ -199,7 +199,7 @@ p_ca <- ggplot(abund@abundance, aes(x = rank, y = p)) +
                     ymax = upper, fill = sample_id), alpha = 0.4) +
     geom_line(aes(color = sample_id)) +
     ggtitle(abund_main) +
-    xlab("Rank") + ylab("Abundance") +
+    xlab("log(Rank)") + ylab("Abundance") +
     scale_x_log10(limits = NULL,
                 breaks = scales::trans_breaks("log10", function(x) 10^x),
                 labels = scales::trans_format("log10", scales::math_format(10^.x))) +

diff --git a/modules/local/airrflow_report/airrflow_report.nf b/modules/local/airrflow_report/airrflow_report.nf
@@ -2,10 +2,10 @@ process AIRRFLOW_REPORT {
     tag "${meta.id}"
     label 'process_high'
 
-    conda "bioconda::r-enchantr=0.1.0"
+    conda "bioconda::r-enchantr=0.1.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.0--r42hdfd78af_2':
-        'quay.io/biocontainers/r-enchantr:0.1.0--r42hdfd78af_2' }"
+        'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.1--r42hdfd78af_0':
+        'quay.io/biocontainers/r-enchantr:0.1.1--r42hdfd78af_0' }"
 
     input:
     tuple val(meta), path(tab) // sequence tsv table in AIRR format

diff --git a/modules/local/enchantr/collapse_duplicates.nf b/modules/local/enchantr/collapse_duplicates.nf
@@ -4,10 +4,10 @@ process COLLAPSE_DUPLICATES {
     label 'process_long_parallelized'
     label 'immcantation'
 
-    conda "bioconda::r-enchantr=0.1.0"
+    conda "bioconda::r-enchantr=0.1.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.0--r42hdfd78af_2':
-        'quay.io/biocontainers/r-enchantr:0.1.0--r42hdfd78af_2' }"
+        'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.1--r42hdfd78af_0':
+        'quay.io/biocontainers/r-enchantr:0.1.1--r42hdfd78af_0' }"
 
     input:
     tuple val(meta), path(tabs) // tuple [val(meta), sequence tsv in AIRR format ]

diff --git a/modules/local/enchantr/define_clones.nf b/modules/local/enchantr/define_clones.nf
@@ -21,10 +21,10 @@ process DEFINE_CLONES {
     label 'process_long_parallelized'
     label 'immcantation'
 
-    conda "bioconda::r-enchantr=0.1.0"
+    conda "bioconda::r-enchantr=0.1.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.0--r42hdfd78af_2':
-        'quay.io/biocontainers/r-enchantr:0.1.0--r42hdfd78af_2' }"
+        'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.1--r42hdfd78af_0':
+        'quay.io/biocontainers/r-enchantr:0.1.1--r42hdfd78af_0' }"
 
     input:
     tuple val(meta), path(tabs) // meta, sequence tsv in AIRR format

diff --git a/modules/local/enchantr/detect_contamination.nf b/modules/local/enchantr/detect_contamination.nf
@@ -5,10 +5,10 @@ process DETECT_CONTAMINATION {
     label 'immcantation'
 
 
-    conda "bioconda::r-enchantr=0.1.0"
+    conda "bioconda::r-enchantr=0.1.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.0--r42hdfd78af_2':
-        'quay.io/biocontainers/r-enchantr:0.1.0--r42hdfd78af_2' }"
+        'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.1--r42hdfd78af_0':
+        'quay.io/biocontainers/r-enchantr:0.1.1--r42hdfd78af_0' }"
 
     input:
     path(tabs)

diff --git a/modules/local/enchantr/dowser_lineages.nf b/modules/local/enchantr/dowser_lineages.nf
@@ -22,10 +22,10 @@ process DOWSER_LINEAGES {
     label 'error_ignore'
     label 'immcantation'
 
-    conda "bioconda::r-enchantr=0.1.0"
+    conda "bioconda::r-enchantr=0.1.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.0--r42hdfd78af_2':
-        'quay.io/biocontainers/r-enchantr:0.1.0--r42hdfd78af_2' }"
+        'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.1--r42hdfd78af_0':
+        'quay.io/biocontainers/r-enchantr:0.1.1--r42hdfd78af_0' }"
 
     input:
     //tuple val(meta), path(tabs) // sequence tsv in AIRR format

diff --git a/modules/local/enchantr/find_threshold.nf b/modules/local/enchantr/find_threshold.nf
@@ -4,10 +4,10 @@ process FIND_THRESHOLD {
     label 'process_long_parallelized'
     label 'immcantation'
 
-    conda "bioconda::r-enchantr=0.1.0"
+    conda "bioconda::r-enchantr=0.1.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.0--r42hdfd78af_2':
-        'quay.io/biocontainers/r-enchantr:0.1.0--r42hdfd78af_2' }"
+        'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.1--r42hdfd78af_0':
+        'quay.io/biocontainers/r-enchantr:0.1.1--r42hdfd78af_0' }"
 
 
     input:

diff --git a/modules/local/enchantr/remove_chimeric.nf b/modules/local/enchantr/remove_chimeric.nf
@@ -5,10 +5,10 @@ process REMOVE_CHIMERIC {
     label 'immcantation'
 
 
-    conda "bioconda::r-enchantr=0.1.0"
+    conda "bioconda::r-enchantr=0.1.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.0--r42hdfd78af_2':
-        'quay.io/biocontainers/r-enchantr:0.1.0--r42hdfd78af_2' }"
+        'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.1--r42hdfd78af_0':
+        'quay.io/biocontainers/r-enchantr:0.1.1--r42hdfd78af_0' }"
 
 
     input:

diff --git a/modules/local/enchantr/report_file_size.nf b/modules/local/enchantr/report_file_size.nf
@@ -6,10 +6,10 @@ process REPORT_FILE_SIZE {
     label 'immcantation'
     label 'single_cpu'
 
-    conda "bioconda::r-enchantr=0.1.0"
+    conda "bioconda::r-enchantr=0.1.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.0--r42hdfd78af_2':
-        'quay.io/biocontainers/r-enchantr:0.1.0--r42hdfd78af_2' }"
+        'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.1--r42hdfd78af_0':
+        'quay.io/biocontainers/r-enchantr:0.1.1--r42hdfd78af_0' }"
 
     input:
     path logs

diff --git a/modules/local/enchantr/single_cell_qc.nf b/modules/local/enchantr/single_cell_qc.nf
@@ -20,10 +20,10 @@ process SINGLE_CELL_QC {
     label 'immcantation'
     label 'process_medium'
 
-    conda "bioconda::r-enchantr=0.1.0"
+    conda "bioconda::r-enchantr=0.1.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.0--r42hdfd78af_2':
-        'quay.io/biocontainers/r-enchantr:0.1.0--r42hdfd78af_2' }"
+        'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.1--r42hdfd78af_0':
+        'quay.io/biocontainers/r-enchantr:0.1.1--r42hdfd78af_0' }"
 
     input:
     path(tabs)

diff --git a/modules/local/enchantr/validate_input.nf b/modules/local/enchantr/validate_input.nf
@@ -6,10 +6,10 @@ process VALIDATE_INPUT {
     label 'immcantation'
     label 'single_cpu'
 
-    conda "bioconda::r-enchantr=0.1.0"
+    conda "bioconda::r-enchantr=0.1.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.0--r42hdfd78af_2':
-        'quay.io/biocontainers/r-enchantr:0.1.0--r42hdfd78af_2' }"
+        'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.1--r42hdfd78af_0':
+        'quay.io/biocontainers/r-enchantr:0.1.1--r42hdfd78af_0' }"
 
     input:
     file samplesheet

diff --git a/modules/local/reveal/add_meta_to_tab.nf b/modules/local/reveal/add_meta_to_tab.nf
@@ -3,10 +3,10 @@ process ADD_META_TO_TAB {
     label 'immcantation'
     label 'single_cpu'
 
-    conda "bioconda::r-enchantr=0.1.0"
+    conda "bioconda::r-enchantr=0.1.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.0--r42hdfd78af_2':
-        'quay.io/biocontainers/r-enchantr:0.1.0--r42hdfd78af_2' }"
+        'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.1--r42hdfd78af_0':
+        'quay.io/biocontainers/r-enchantr:0.1.1--r42hdfd78af_0' }"
 
     cache 'deep' // Without 'deep' this process would run when using -resume
 

diff --git a/modules/local/reveal/filter_junction_mod3.nf b/modules/local/reveal/filter_junction_mod3.nf
@@ -3,10 +3,10 @@ process FILTER_JUNCTION_MOD3 {
     label 'immcantation'
     label 'single_cpu'
 
-    conda "bioconda::r-enchantr=0.1.0"
+    conda "bioconda::r-enchantr=0.1.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.0--r42hdfd78af_2':
-        'quay.io/biocontainers/r-enchantr:0.1.0--r42hdfd78af_2' }"
+        'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.1--r42hdfd78af_0':
+        'quay.io/biocontainers/r-enchantr:0.1.1--r42hdfd78af_0' }"
 
     input:
     tuple val(meta), path(tab) // sequence tsv in AIRR format

diff --git a/modules/local/reveal/filter_quality.nf b/modules/local/reveal/filter_quality.nf
@@ -3,10 +3,10 @@ process FILTER_QUALITY {
     label 'immcantation'
     label 'single_cpu'
 
-    conda "bioconda::r-enchantr=0.1.0"
+    conda "bioconda::r-enchantr=0.1.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.0--r42hdfd78af_2':
-        'quay.io/biocontainers/r-enchantr:0.1.0--r42hdfd78af_2' }"
+        'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.1--r42hdfd78af_0':
+        'quay.io/biocontainers/r-enchantr:0.1.1--r42hdfd78af_0' }"
 
     input:
     tuple val(meta), path(tab) // sequence tsv in AIRR format