Feature/wrabbit

requirements.txt

@@ -1,5 +1,6 @@
 ruamel.yaml >= 0.16
 sevenbridges-python >= 2.0
 nf-core==2.1
+wrabbit==0.1.1
 cwlformat
 packaging

sbpack/noncwl/Readme.md

@@ -51,18 +51,21 @@ $ sbpack_nf -h
 
 usage: sbpack_nf [-h]
                  [--profile PROFILE]
-                 --appid APPID 
+                 [--appid APPID]
                  --workflow-path WORKFLOW_PATH
                  [--entrypoint ENTRYPOINT]
                  [--sb-package-id SB_PACKAGE_ID]
                  [--sb-doc SB_DOC]
                  [--dump-sb-app]
-                 [--no-package]
                  [--executor-version EXECUTOR_VERSION]
                  [--execution-mode {single-instance,multi-instance}]
                  [--json]
                  [--sb-schema SB_SCHEMA]
                  [--revision-note REVISION_NOTE]
+                 [--app-name APP_NAME]
+                 [--exclude EXCLUDE [EXCLUDE ...]]
+                 [--sample-sheet-schema SAMPLE_SHEET_SCHEMA]
+                 [--auto]
 
 optional arguments:
   -h, --help            show this help message and exit
@@ -79,24 +82,41 @@ optional arguments:
                         than one '*.nf' script is detected, an error is
                         raised.
   --sb-package-id SB_PACKAGE_ID
-                        Id of an already uploaded package
+                        Id of an already uploaded package.
   --sb-doc SB_DOC       Path to a doc file for sb app. If not provided,
                         README.md will be used if available
   --dump-sb-app         Dump created sb app to file if true and exit
-  --no-package          Only provide a sb app schema and a git URL for
-                        entrypoint
   --executor-version EXECUTOR_VERSION
                         Version of the Nextflow executor to be used with the
                         app.
   --execution-mode {single-instance,multi-instance}
-                        Execution mode for your application.
+                        Execution mode for your application. Can be multi-
+                        instance or single-instance
   --json                Dump sb app schema in JSON format (YAML by default)
   --sb-schema SB_SCHEMA
                         Do not create new schema, use this schema file. It is
                         sb_nextflow_schema in JSON or YAML format.
   --revision-note REVISION_NOTE
                         Revision note to be placed in the CWL schema if the
                         app is uploaded to the sbg platform.
+  --app-name APP_NAME   Name of the app to be shown on the platform.
+  --exclude EXCLUDE [EXCLUDE ...]
+                        Glob patterns you want to exclude from the code
+                        package. By default the following patterns are
+                        excluded: ['*.git', '*.git*', '.git', '.git*', 'work',
+                        '.nextflow.log', '.DS_Store', '.devcontainer',
+                        '.editorconfig', '.gitattributes', '.nextflow', '.pre-
+                        commit-config.yaml', '.prettierignore',
+                        '.prettierrc.yml', '.idea', '.pytest_cache', '*.egg-
+                        info']
+  --sample-sheet-schema SAMPLE_SHEET_SCHEMA
+                        Path to the sample sheet schema yaml. The sample sheet
+                        schema should contain the following keys:
+                        'sample_sheet_input', 'sample_sheet_name', 'header',
+                        'rows', 'defaults', 'group_by', 'format_'
+  --auto                Automatically detect all possible inputs directly from
+                        the --workflow-path location
+
 ```
 ### Example
 
@@ -147,4 +167,60 @@ sbcopy --appid division-name/project-name/app-name --projectid division-name/des
 Copying an app from one division to another.
 ```
 sbcopy --profile source_division target_division --appid source-division-name/project-name/app-name --projectid target-division-name/destination-project-name
-```
+```
+
+# sbmanifest
+
+Developed to help remap file paths contained within a manifest file to platform
+file locations. This is useful when utilizing sample sheets to run nextflow
+pipelines on SB powered platforms.
+
+### Usage
+
+```
+usage: sbmanifest [-h] [--profile PROFILE] --projectid PROJECTID
+                  --sample-sheet SAMPLE_SHEET --columns string [string ...]
+                  [--output OUTPUT] [--upload] [--tags string [string ...]]
+                  [--validate]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --profile PROFILE     SB platform profile as set in the SB API credentials
+                        file.
+  --projectid PROJECTID
+                        Takes the form {user or division}/{project}.
+  --sample-sheet SAMPLE_SHEET
+                        Path to the sample sheet.
+  --columns string [string ...]
+                        Specify columns that contain paths to files on the
+                        platformas a list of strings separated by spaces.
+  --output OUTPUT, -o OUTPUT
+                        Name of the output file.
+  --upload, -u          Upload the file to the project after making it.
+  --tags string [string ...]
+                        Specify tags that you want the sample sheet to have on
+                        the platform, after it is uploaded.
+  --validate            Validate if each file exists on target project
+                        location.
+```
+
+### Examples
+
+Remap a sample sheet and upload it to the platform with the tag "SampleSheet"
+```
+sbmanifest --projectid user/project_id --sample-sheet /path/to/rnaseq_samplesheet.csv --columns fastq_1 fastq_2 -o rnaseq_samplesheet.csv -u --tags SampleSheet
+```
+Given the contents of this sample sheet is:
+
+| sample  | fastq_1                          | fastq_2                          | strandedness |
+|:--------|:---------------------------------|:---------------------------------|:-------------|
+| SAMPLE1 | RNAseq_inputs/SAMPLE1_1.fastq.gz | RNAseq_inputs/SAMPLE1_2.fastq.gz | reverse      |
+| SAMPLE2 | RNAseq_inputs/SAMPLE2_1.fastq.gz | RNAseq_inputs/SAMPLE2_2.fastq.gz | reverse      |
+
+
+Remapped file will be:
+
+| sample  | fastq_1                                                           | fastq_2                                                           | strandedness |
+|:--------|:------------------------------------------------------------------|:------------------------------------------------------------------|:-------------|
+| SAMPLE1 | vs:///Projects/project-root-uuid/RNAseq_inputs/SAMPLE1_1.fastq.gz | vs:///Projects/project-root-uuid/RNAseq_inputs/SAMPLE1_2.fastq.gz | reverse      |
+| SAMPLE2 | vs:///Projects/project-root-uuid/RNAseq_inputs/SAMPLE2_1.fastq.gz | vs:///Projects/project-root-uuid/RNAseq_inputs/SAMPLE2_2.fastq.gz | reverse      |

sbpack/noncwl/__init__.py

@@ -1,9 +0,0 @@
-import os
-
-PACKAGE_PATH = os.path.abspath(os.path.dirname(__file__))
-JS_PATH = os.path.join(PACKAGE_PATH, 'js_templates')
-
-
-def read_js_template(file_name):
-    with open(os.path.join(JS_PATH, file_name), 'r') as f:
-        return f.read()

sbpack/noncwl/constants.py

@@ -1,7 +1,3 @@
-from enum import Enum
-from sbpack.noncwl import read_js_template
-
-
 # ############################## Generic Bits ############################### #
 PACKAGE_SIZE_LIMIT = 100 * 1024 * 1024  # 100 MB
 REMOVE_INPUT_KEY = "REMOVE_THIS_KEY"
@@ -22,8 +18,6 @@ class EXTENSIONS:
 # ############################ CWL Standard Bits ############################ #
 # A generic SB input array of files that should be available on the
 # instance but are not explicitly provided to the execution as wdl params.
-SAMPLE_SHEET_FUNCTION = read_js_template("sample_sheet_generator.js")
-SAMPLE_SHEET_SWITCH = read_js_template("sample_sheet_switch.js")
 
 GENERIC_FILE_ARRAY_INPUT = {
     "id": "auxiliary_files",
@@ -41,18 +35,6 @@ class EXTENSIONS:
            "that is required for workflow execution."
 }
 
-GENERIC_NF_OUTPUT_DIRECTORY = {
-    "id": "nf_workdir",
-    "type": "Directory?",
-    "label": "Work Directory",
-    "doc": "This is a template output. "
-           "Please change glob to directories specified in "
-           "publishDir in the workflow.",
-    "outputBinding": {
-        "glob": "work"
-    }
-}
-
 GENERIC_WDL_OUTPUT_DIRECTORY = {
     "id": "output_txt",
     "doc": "This is a template output. "
@@ -84,62 +66,27 @@ class EXTENSIONS:
     AUX_FILES_REQUIREMENT
 ]
 
-
-def sample_sheet(
-        file_name, sample_sheet_input, format_, input_source, header, rows,
-        defaults, group_by):
-    basename = ".".join(file_name.split(".")[:-1])
-    ext = file_name.split(".")[-1]
-    new_name = f"{basename}.new.{ext}"
-
-    return {
-        "class": "InitialWorkDirRequirement",
-        "listing": [
-            {
-                "entryname": f"${{ return {sample_sheet_input} ? {sample_sheet_input}.nameroot + '.new' + {sample_sheet_input}.nameext : '{file_name}' }}",
-                "entry": SAMPLE_SHEET_FUNCTION.format_map(locals()),
-                "writable": False
-            }
-        ]
-    }
-
-
-# ############################## Nextflow Bits ############################## #
-# Keys that should be skipped when parsing nextflow tower yaml file
-
-NF_SCHEMA_DEFAULT_NAME = 'nextflow_schema.json'
-SB_SCHEMA_DEFAULT_NAME = 'sb_nextflow_schema'
-
-# Mappings of nextflow input fields to SB input fields
-#  nextflow_key: cwl_key mapping
-NF_TO_CWL_PORT_MAP = {
-    'default': 'sbg:toolDefaultValue',
-    'description': 'label',
-    'help_text': 'doc',
-    'mimetype': 'format',
-    'fa_icon': 'sbg:icon',
-    'pattern': 'sbg:pattern',
-    'hidden': 'sbg:hidden',
-}
-
-# Mappings of nextflow definition fields to SB category fields
-#  nextflow_key: cwl_key mapping
-NF_TO_CWL_CATEGORY_MAP = {
-    'title': 'sbg:title',
-    'description': 'sbg:doc',
-    'fa_icon': 'sbg:icon',
-}
-
-# What keys to skip from the tower.yml file
-SKIP_NEXTFLOW_TOWER_KEYS = [
-    'tower',
-    'mail',
+# Nextflow
+DEFAULT_EXCLUDE_PATTERNS = [
+    "*.git",
+    "*.git*",
+    ".git",
+    ".git*",
+    # ".github",
+    # ".gitignore",
+    # ".gitpod.yml",
+    "work",
+    ".nextflow.log",
+    ".DS_Store",
+    ".devcontainer",
+    ".editorconfig",
+    ".gitattributes",
+    ".nextflow",
+    # ".nf-core.yml",
+    ".pre-commit-config.yaml",
+    ".prettierignore",
+    ".prettierrc.yml",
+    ".idea",
+    ".pytest_cache",
+    "*.egg-info",
 ]
-
-
-class ExecMode(Enum):
-    single = 'single-instance'
-    multi = 'multi-instance'
-
-    def __str__(self):
-        return self.value