Some fixes on top of feature/support-external-data

README.md

@@ -29,6 +29,7 @@ Input/output options
   --study_accession                       [string]  The ENA Study secondary accession
   --reads_accession                       [string]  The ENA Run primary accession
   --private_study                         [boolean] To use if the ENA study is private
+  --samplesheet                           [string]  Path to comma-separated file containing information about the raw reads with the prefix to be used.
   --assembler                             [string]  The short reads assembler (accepted: spades, metaspades, megahit)
   --single_end                            [boolean] Force the single_end value for the study / reads
   --library_strategy                      [string]  Force the library_strategy value for the study / reads (accepted: metagenomic, metatranscriptomic,

assets/schema_input.json

@@ -44,8 +44,13 @@
                 "type": "string",
                 "enum": ["metagenomic", "metatranscriptomic", "genomic", "transcriptomic", "other"],
                 "errorMessage": "library strategy should be only value from list: 'metagenomic', 'metatranscriptomic', 'genomic', 'transcriptomic', 'other'"
+            },
+            "assembly_memory": {
+                "type": "integer",
+                "default": null,
+                "description": "Default memory allocated for the assembly process for the run."
             }
         },
-        "required": ["study_accession","reads_accession", "fastq_1", "library_layout", "library_strategy"]
+        "required": ["study_accession", "reads_accession", "fastq_1", "library_layout", "library_strategy"]
     }
 }

conf/modules.config

@@ -41,7 +41,7 @@ process {
                         ]
                         def output_file = new File(filename);
                         if ( file_patterns_to_publish.any { output_file.name.contains(it) } ) {
-                            return "${study_reads_folder()}/qc/fastp/${output_file.name}";
+                            return "${study_reads_folder( meta )}/qc/fastp/${output_file.name}";
                         }
                         return null;
                     }
@@ -65,7 +65,7 @@ process {
                             return null;
                         }
                         def output_file = new File(filename);
-                        return "${study_reads_folder()}/qc/fastqc/${output_file.name}";
+                        return "${study_reads_folder( meta )}/qc/fastqc/${output_file.name}";
                     }
                 }
             ]
@@ -128,7 +128,7 @@ process {
                         ]
                         def output_file = new File(filename);
                         if ( file_patterns_to_publish.any { output_file.name.contains(it) } ) {
-                            return "${study_reads_folder()}/assembly/${meta.assembler}/${meta.assembler_version}/${output_file.name}";
+                            return "${study_reads_folder( meta )}/assembly/${meta.assembler}/${meta.assembler_version}/${output_file.name}";
                         }
                         return null;
                     }
@@ -153,7 +153,7 @@ process {
                 saveAs: {
                     filename -> {
                         def output_file = new File(filename);
-                        return "${study_reads_folder()}/assembly/${meta.assembler}/${meta.assembler_version}/${output_file.name}";
+                        return "${study_reads_folder( meta )}/assembly/${meta.assembler}/${meta.assembler_version}/${output_file.name}";
                     }
                 }
             ]
@@ -206,7 +206,7 @@ process {
                 saveAs: {
                     filename -> {
                         def output_file = new File(filename);
-                        return "${study_reads_folder()}/assembly/${meta.assembler}/${meta.assembler_version}/decontamination/${output_file.name}";
+                        return "${study_reads_folder( meta )}/assembly/${meta.assembler}/${meta.assembler_version}/decontamination/${output_file.name}";
                     }
                 }
             ]
@@ -231,7 +231,7 @@ process {
                             return null;
                         }
                         def output_file = new File(filename);
-                        return "${study_reads_folder()}/assembly/${meta.assembler}/${meta.assembler_version}/${output_file.simpleName}_filtered_contigs.${output_file.extension}";
+                        return "${study_reads_folder( meta )}/assembly/${meta.assembler}/${meta.assembler_version}/${output_file.simpleName}_filtered_contigs.${output_file.extension}";
                     }
                 }
             ]
@@ -256,7 +256,7 @@ process {
                 saveAs: {
                     filename -> {
                         def output_file = new File(filename);
-                        return "${study_reads_folder()}/assembly/${meta.assembler}/${meta.assembler_version}/coverage/${output_file.name}";
+                        return "${study_reads_folder( meta )}/assembly/${meta.assembler}/${meta.assembler_version}/coverage/${output_file.name}";
                     }
                 }
             ]
@@ -301,7 +301,7 @@ process {
                             return null;
                         }
                         def output_file = new File(filename);
-                        return "${study_reads_folder()}/assembly/${meta.assembler}/${meta.assembler_version}/qc/multiqc/${output_file.name}";
+                        return "${study_reads_folder( meta )}/assembly/${meta.assembler}/${meta.assembler_version}/qc/multiqc/${output_file.name}";
                     }
                 }
             ]
@@ -324,7 +324,7 @@ process {
                             return null;
                         }
                         def output_file = new File(filename);
-                        return "${study_reads_folder()}/assembly/${meta.assembler}/${meta.assembler_version}/qc/quast/${output_file.name}";
+                        return "${study_reads_folder( meta )}/assembly/${meta.assembler}/${meta.assembler_version}/qc/quast/${output_file.name}";
                     }
                 }
             ]

modules.json

@@ -24,18 +24,14 @@
                     "blast/blastn": {
                         "branch": "master",
                         "git_sha": "209e5a3e2753c5e628736a662c877c20f341ee15",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/blast/blastn/blast-blastn.diff"
                     },
                     "bwamem2/index": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
-                    "bwamem2/mem": {
-                        "branch": "master",
-                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
-                        "installed_by": ["modules"]
-                    },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e",

modules/ebi-metagenomics/bwamem2/mem/main.nf

@@ -7,8 +7,7 @@ process BWAMEM2_MEM {
         'biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:2d15960ccea84e249a150b7f5d4db3a42fc2d6c3-0' }"
 
     input:
-    tuple val(meta), path(reads)
-    tuple val(meta2), path(index)
+    tuple val(meta), path(reads), path(index)
 
     output:
     tuple val(meta), path("*_sorted.bam"), path("*_sorted.bam.bai"), emit: bam
@@ -21,7 +20,6 @@ process BWAMEM2_MEM {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: meta.id
-    def database = task.ext.database ?: meta2.id
     """
     INDEX=`find -L ./ -name "*.amb" | sed 's/\\.amb\$//'`